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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN TLR4-HUMAN MD-2-E.COLI LPS RA COMPLEX

Authors :   B. S. Park, D. H. Song, H. M. Kim, J. -O. Lee

Date :   21 Jan 09 (Deposition) - 03 Mar 09 (Release) - 20 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Leucine Rich Repeat, Glycoprotein, Immune Response, Inflammatory Response, Innate Immunity, Membrane, Receptor, Transmembrane, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. S. Park, D. H. Song, H. M. Kim, B. -S. Choi, H. Lee, J. -O. Lee
The Structural Basis Of Lipopolysaccharide Recognition By The Tlr4-Md-2 Complex
Nature V. 458 1191 2009
PubMed-ID: 19252480 | Reference-DOI: 10.1038/NATURE07830

Molecule 1 - TOLL-LIKE RECEPTOR 4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell	:	HIGH FIVE CELLS
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	EXTRACELLULAR DOMAIN, RESIDUES 27-631
	Gene	:	TLR4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TLR4, HTOLL

Molecule 2 - LYMPHOCYTE ANTIGEN 96
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell	:	HIGH FIVE CELLS
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	ESOP1, LY96, MD-2, MD2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MD-2, PROTEIN MD-2, ESOP-1

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (10, 52)

No.	Name	Count	Type	Full Name
1	DAO	2	Ligand/Ion	LAURIC ACID
2	FTT	8	Ligand/Ion	3-HYDROXY-TETRADECANOIC ACID
3	GCS	1	Ligand/Ion	D-GLUCOSAMINE
4	GMH	6	Ligand/Ion	L-GLYCERO-D-MANNO-HEPTOPYRANOSE
5	KDO	4	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
6	MG	2	Ligand/Ion	MAGNESIUM ION
7	MYR	2	Ligand/Ion	MYRISTIC ACID
8	NAG	16	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
9	PA1	3	Ligand/Ion	2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE
10	PO4	8	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (52, 52)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PA1 A:1002 , FTT A:1005 , FTT A:1006 , PO4 A:1010 , KDO A:1012 , SER C:120	BINDING SITE FOR RESIDUE PA1 A 1001
02	AC2	SOFTWARE	PA1 A:1001 , FTT A:1003 , FTT A:1004 , FTT A:1005 , PO4 A:1011 , LYS C:122	BINDING SITE FOR RESIDUE PA1 A 1002
03	AC3	SOFTWARE	TYR A:296 , LYS A:341 , PA1 A:1001 , KDO A:1013 , GMH A:1014 , GMH A:1015 , GMH A:1016	BINDING SITE FOR RESIDUE KDO A 1012
04	AC4	SOFTWARE	KDO A:1012 , GMH A:1016 , PO4 A:1018 , LYS C:58	BINDING SITE FOR RESIDUE KDO A 1013
05	AC5	SOFTWARE	PO4 A:1011 , KDO A:1012 , GMH A:1015 , PO4 A:1018	BINDING SITE FOR RESIDUE GMH A 1014
06	AC6	SOFTWARE	TYR A:296 , KDO A:1012 , GMH A:1014 , GMH A:1016 , PO4 A:1017	BINDING SITE FOR RESIDUE GMH A 1015
07	AC7	SOFTWARE	ASP A:294 , KDO A:1012 , KDO A:1013 , GMH A:1015	BINDING SITE FOR RESIDUE GMH A 1016
08	AC8	SOFTWARE	PA1 A:1002 , GLN B:436 , VAL C:82 , LEU C:87 , SER C:127 , TYR C:131	BINDING SITE FOR RESIDUE FTT A 1003
09	AC9	SOFTWARE	PA1 A:1002 , PHE C:121 , LYS C:122 , ILE C:124 , PHE C:151	BINDING SITE FOR RESIDUE FTT A 1004
10	BC1	SOFTWARE	PA1 A:1001 , PA1 A:1002 , DAO A:1007 , PHE C:119 , PHE C:151	BINDING SITE FOR RESIDUE FTT A 1005
11	BC2	SOFTWARE	ARG A:264 , PA1 A:1001 , MYR A:1008 , PO4 A:1010 , TYR C:65 , LEU C:71 , PHE C:104 , ILE C:117 , SER C:118 , PHE C:119	BINDING SITE FOR RESIDUE FTT A 1006
12	BC3	SOFTWARE	FTT A:1005 , ARG C:90 , TYR C:131	BINDING SITE FOR RESIDUE DAO A 1007
13	BC4	SOFTWARE	FTT A:1006 , ILE C:46 , ILE C:63 , PHE C:76 , GLU C:92	BINDING SITE FOR RESIDUE MYR A 1008
14	BC5	SOFTWARE	ARG A:264 , PA1 A:1001 , FTT A:1006 , MG A:2001 , SER C:118	BINDING SITE FOR RESIDUE PO4 A 1010
15	BC6	SOFTWARE	PA1 A:1002 , GMH A:1014	BINDING SITE FOR RESIDUE PO4 A 1011
16	BC7	SOFTWARE	GMH A:1015	BINDING SITE FOR RESIDUE PO4 A 1017
17	BC8	SOFTWARE	KDO A:1013 , GMH A:1014	BINDING SITE FOR RESIDUE PO4 A 1018
18	BC9	SOFTWARE	HIS A:148 , ASN A:173	BINDING SITE FOR RESIDUE NAG A 711
19	CC1	SOFTWARE	GLU A:178 , HIS A:179 , ASN A:205 , SER A:207	BINDING SITE FOR RESIDUE NAG A 721
20	CC2	SOFTWARE	SER A:504 , GLN A:505 , ASN A:526 , ASP A:550 , NAG A:732 , NAG A:761	BINDING SITE FOR RESIDUE NAG A 731
21	CC3	SOFTWARE	NAG A:731 , NAG A:761 , NAG A:762	BINDING SITE FOR RESIDUE NAG A 732
22	CC4	SOFTWARE	ASN A:497 , ASP A:614	BINDING SITE FOR RESIDUE NAG A 741
23	CC5	SOFTWARE	ASP A:550 , ASN A:575 , THR A:577 , NAG A:731 , NAG A:732 , NAG A:762	BINDING SITE FOR RESIDUE NAG A 761
24	CC6	SOFTWARE	NAG A:732 , NAG A:761	BINDING SITE FOR RESIDUE NAG A 762
25	CC7	SOFTWARE	HOH A:1 , ASP A:294 , PO4 A:1010	BINDING SITE FOR RESIDUE MG A 2001
26	CC8	SOFTWARE	PA1 B:1002 , FTT B:1005 , FTT B:1006 , PO4 B:1010 , KDO B:1012 , SER D:120	BINDING SITE FOR RESIDUE GCS B 1001
27	CC9	SOFTWARE	GCS B:1001 , FTT B:1003 , FTT B:1004 , FTT B:1005 , PO4 B:1011 , LYS D:122	BINDING SITE FOR RESIDUE PA1 B 1002
28	DC1	SOFTWARE	TYR B:296 , LYS B:341 , GCS B:1001 , KDO B:1013 , GMH B:1014 , GMH B:1015 , GMH B:1016	BINDING SITE FOR RESIDUE KDO B 1012
29	DC2	SOFTWARE	KDO B:1012 , GMH B:1016 , PO4 B:1018 , LYS D:58	BINDING SITE FOR RESIDUE KDO B 1013
30	DC3	SOFTWARE	PO4 B:1011 , KDO B:1012 , GMH B:1015 , PO4 B:1018	BINDING SITE FOR RESIDUE GMH B 1014
31	DC4	SOFTWARE	TYR B:296 , KDO B:1012 , GMH B:1014 , GMH B:1016 , PO4 B:1017	BINDING SITE FOR RESIDUE GMH B 1015
32	DC5	SOFTWARE	ASP B:294 , KDO B:1012 , KDO B:1013 , GMH B:1015	BINDING SITE FOR RESIDUE GMH B 1016
33	DC6	SOFTWARE	GLN A:436 , PA1 B:1002 , VAL D:82 , LEU D:87 , SER D:127 , TYR D:131	BINDING SITE FOR RESIDUE FTT B 1003
34	DC7	SOFTWARE	PA1 B:1002 , PHE D:121 , LYS D:122 , ILE D:124 , PHE D:151	BINDING SITE FOR RESIDUE FTT B 1004
35	DC8	SOFTWARE	GCS B:1001 , PA1 B:1002 , DAO B:1007 , PHE D:119 , PHE D:151	BINDING SITE FOR RESIDUE FTT B 1005
36	DC9	SOFTWARE	ARG B:264 , GCS B:1001 , MYR B:1008 , PO4 B:1010 , TYR D:65 , LEU D:71 , PHE D:104 , ILE D:117 , SER D:118 , PHE D:119	BINDING SITE FOR RESIDUE FTT B 1006
37	EC1	SOFTWARE	FTT B:1005 , MYR B:1008 , ARG D:90	BINDING SITE FOR RESIDUE DAO B 1007
38	EC2	SOFTWARE	FTT B:1006 , DAO B:1007 , ILE D:46 , ILE D:63 , PHE D:76 , GLU D:92	BINDING SITE FOR RESIDUE MYR B 1008
39	EC3	SOFTWARE	ARG B:264 , GCS B:1001 , FTT B:1006 , MG B:2001 , SER D:118	BINDING SITE FOR RESIDUE PO4 B 1010
40	EC4	SOFTWARE	PA1 B:1002 , GMH B:1014	BINDING SITE FOR RESIDUE PO4 B 1011
41	EC5	SOFTWARE	ARG B:322 , GMH B:1015	BINDING SITE FOR RESIDUE PO4 B 1017
42	EC6	SOFTWARE	KDO B:1013 , GMH B:1014	BINDING SITE FOR RESIDUE PO4 B 1018
43	EC7	SOFTWARE	ASN B:173	BINDING SITE FOR RESIDUE NAG B 811
44	EC8	SOFTWARE	GLU B:178 , HIS B:179 , ASN B:205	BINDING SITE FOR RESIDUE NAG B 821
45	EC9	SOFTWARE	SER B:504 , GLN B:505 , ASN B:526 , ASP B:550 , NAG B:832 , NAG B:861 , NAG B:862	BINDING SITE FOR RESIDUE NAG B 831
46	FC1	SOFTWARE	NAG B:831 , NAG B:861 , NAG B:862	BINDING SITE FOR RESIDUE NAG B 832
47	FC2	SOFTWARE	SER B:472 , ASN B:497	BINDING SITE FOR RESIDUE NAG B 841
48	FC3	SOFTWARE	ASP B:550 , SER B:552 , PHE B:573 , ASN B:575 , THR B:577 , VAL B:602 , NAG B:831 , NAG B:832 , NAG B:862	BINDING SITE FOR RESIDUE NAG B 861
49	FC4	SOFTWARE	NAG B:831 , NAG B:832 , NAG B:861	BINDING SITE FOR RESIDUE NAG B 862
50	FC5	SOFTWARE	ASP B:294 , PO4 B:1010	BINDING SITE FOR RESIDUE MG B 2001
51	FC6	SOFTWARE	PHE C:64 , ASN C:114	BINDING SITE FOR RESIDUE NAG C 751
52	FC7	SOFTWARE	PHE D:64 , ASN D:114	BINDING SITE FOR RESIDUE NAG D 851

Asymmetric/Biological Unit

No.	Residues
1	A:29	-	A:40
2	A:281	-	A:306
3	A:390	-	A:391
4	A:583	-	A:609
5	A:585	-	A:627
6	B:29	-	B:40
7	B:281	-	B:306
8	B:390	-	B:391
9	B:583	-	B:609
10	B:585	-	B:627
11	C:25	-	C:51
12	C:37	-	C:148
13	C:95	-	C:105
14	D:25	-	D:51
15	D:37	-	D:148
16	D:95	-	D:105

Asymmetric/Biological Unit

No.	Residues
1	Cys A:390	-	Cys A:391
2	Cys B:390	-	Cys B:391
3	Asn C:49	-	Pro C:50
4	Asn D:49	-	Pro D:50

Asymmetric/Biological Unit (17, 34)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_050030	R	56	G	LY96_HUMAN	Polymorphism	6472812	C/D	G	56	G
02	UniProt	VAR_024532	P	157	S	LY96_HUMAN	Polymorphism	11466004	C/D	P	157	S
03	UniProt	VAR_021977	T	175	A	TLR4_HUMAN	Polymorphism	16906079	A/B	T	175	A
04	UniProt	VAR_018729	Q	188	R	TLR4_HUMAN	Polymorphism	5030713	A/B	Q	188	R
05	UniProt	VAR_018730	C	246	S	TLR4_HUMAN	Polymorphism	5030714	A/B	C	246	S
06	UniProt	VAR_074187	E	287	D	TLR4_HUMAN	Polymorphism	---	A/B	E	287	D
07	UniProt	VAR_012739	D	299	G	TLR4_HUMAN	Polymorphism	4986790	A/B	D	299	G
08	UniProt	VAR_047563	C	306	W	TLR4_HUMAN	Polymorphism	2770145	A/B	C	306	W
09	UniProt	VAR_047564	V	310	G	TLR4_HUMAN	Polymorphism	2770144	A/B	V	310	G
10	UniProt	VAR_018731	N	329	S	TLR4_HUMAN	Polymorphism	5030715	A/B	N	329	S
11	UniProt	VAR_020334	F	342	Y	TLR4_HUMAN	Polymorphism	5031050	A/B	F	342	Y
12	UniProt	VAR_037668	L	385	F	TLR4_HUMAN	Polymorphism	11536884	A/B	L	385	F
13	UniProt	VAR_012740	T	399	I	TLR4_HUMAN	Polymorphism	4986791	A/B	T	399	I
14	UniProt	VAR_020335	S	400	N	TLR4_HUMAN	Polymorphism	4987233	A/B	S	400	N
15	UniProt	VAR_018732	F	443	L	TLR4_HUMAN	Polymorphism	5030716	A/B	F	443	L
16	UniProt	VAR_018733	E	474	K	TLR4_HUMAN	Polymorphism	5030718	A/B	E	474	K
17	UniProt	VAR_018734	Q	510	H	TLR4_HUMAN	Polymorphism	5030719	A/B	Q	510	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 22)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	TLR4_HUMAN	55-76 79-100 103-124 176-199 151-172 374-394 400-422 423-444 497-518 521-542 545-565	22	A:55-76 B:55-76 A:79-100 B:79-100 A:103-124 B:103-124 A:176-199 B:176-199 A:151-172 B:151-172 A:374-394 B:374-394 A:400-422 B:400-422 A:423-444 B:423-444 A:497-518 B:497-518 A:521-542 B:521-542 A:545-565 B:545-565

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000284818	1a	ENSE00001244306	chr8:74903587-74903789	203	LY96_HUMAN	1-38	38	2	C:19-38 D:19-38	20 20
1.2	ENST00000284818	2	ENSE00001016737	chr8:74917031-74917120	90	LY96_HUMAN	38-68	31	2	C:38-68 D:38-68	31 31
1.3	ENST00000284818	3	ENSE00001016736	chr8:74922236-74922364	129	LY96_HUMAN	68-111	44	2	C:68-111 D:68-111	44 44
1.4	ENST00000284818	4	ENSE00001016734	chr8:74939024-74939076	53	LY96_HUMAN	111-128	18	2	C:111-128 D:111-128	18 18
1.5b	ENST00000284818	5b	ENSE00002121776	chr8:74941191-74941322	132	LY96_HUMAN	129-160	32	2	C:129-158 D:129-158	30 30

2.1b	ENST00000355622	1b	ENSE00001946124	chr9:120466650-120466843	194	TLR4_HUMAN	1-31	31	2	A:27-31 B:27-31	5 5
2.3a	ENST00000355622	3a	ENSE00001654637	chr9:120470841-120471007	167	TLR4_HUMAN	32-87	56	2	A:32-87 B:32-87	56 56
2.4c	ENST00000355622	4c	ENSE00001462052	chr9:120474667-120479149	4483	TLR4_HUMAN	87-839	753	2	A:87-627 B:87-627	541 541

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:601
 aligned with TLR4_HUMAN | O00206 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:601
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626 
           TLR4_HUMAN    27 EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNITC 627
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee..................eee.....................eee.......ee............eee.......ee............eee.....................eee...........hhhhh......eee.......eehhhhhhhhhhh.....eee.......ee........eeeeeeee....hhhhhhhhhhhh...eeeeeeee...............hhhhhhheeeeeeeeee..........hhhhh...eeeeeee...............eeeee................eeeee.................eee.......eeeeeehhhhh.....eee.....eeeeeeeee......eee....eeehhhhh..........eee.............................hhhhh...........................hhhhh..................hhhhhh........................................hhhhhhhhhhhhhh.....hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------A------------R---------------------------------------------------------S----------------------------------------D-----------G------W---G------------------S------------Y------------------------------------------F-------------IN------------------------------------------L------------------------------K-----------------------------------H--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------LRR  PDB: A:55-76     --LRR  PDB: A:79-100    --LRR  PDB: A:103-124   --------------------------LRR  PDB: A:151-172   ---LRR  PDB: A:176-199     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR  PDB: A:374-394  -----LRR  PDB: A:400-422    LRR  PDB: A:423-444   ----------------------------------------------------LRR  PDB: A:497-518   --LRR  PDB: A:521-542   --LRR  PDB: A:545-565  -------------------------------------------------------------- PROSITE
           Transcript 2 (1) 2.1b Exon 2.3a  PDB: A:32-87 UniProt: 32-87                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 2 (1)
           Transcript 2 (2) ------------------------------------------------------------Exon 2.4c  PDB: A:87-627 UniProt: 87-839 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Transcript 2 (2)
                 3fxi A  27 EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNITC 627
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626

Chain B from PDB  Type:PROTEIN  Length:601
 aligned with TLR4_HUMAN | O00206 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:601
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626 
           TLR4_HUMAN    27 EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNITC 627
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee..................eee.....................eee.......ee............eee.......ee............eee.....................eee...........hhhhhh.....eee.......eehhhhhhhhhhh.....eee.......ee........eeeeeeee....hhhhhhhhhhhh...eeeeeeee...............hhhhhhheeeeeeeeee..........hhhhh...eeeeeee...............eeeee................eeeee.................eee.......eeeeee..........eee.....eeeeeeeee......eee....eeehhhhh..........eee.............................hhhhh...........................hhhhh..................hhhhhh........................................hhhhhhhhhhhhhh.....hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------A------------R---------------------------------------------------------S----------------------------------------D-----------G------W---G------------------S------------Y------------------------------------------F-------------IN------------------------------------------L------------------------------K-----------------------------------H--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------LRR  PDB: B:55-76     --LRR  PDB: B:79-100    --LRR  PDB: B:103-124   --------------------------LRR  PDB: B:151-172   ---LRR  PDB: B:176-199     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR  PDB: B:374-394  -----LRR  PDB: B:400-422    LRR  PDB: B:423-444   ----------------------------------------------------LRR  PDB: B:497-518   --LRR  PDB: B:521-542   --LRR  PDB: B:545-565  -------------------------------------------------------------- PROSITE
           Transcript 2 (1) 2.1b Exon 2.3a  PDB: B:32-87 UniProt: 32-87                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 2 (1)
           Transcript 2 (2) ------------------------------------------------------------Exon 2.4c  PDB: B:87-627 UniProt: 87-839 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Transcript 2 (2)
                 3fxi B  27 EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNITC 627
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626

Chain C from PDB  Type:PROTEIN  Length:140
 aligned with LY96_HUMAN | Q9Y6Y9 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:140
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158
           LY96_HUMAN    19 QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKRSKGLLHIFYIPRRDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPN 158
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeeee........eeeee..........eeeeee.........eeeeeeee..ee...eeee........hhhhhh.....eeeeee..........eeeeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------G----------------------------------------------------------------------------------------------------S- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a           -----------------------------Exon 1.3  PDB: C:68-111 UniProt: 68-111     -----------------Exon 1.5b  PDB: C:129-158      Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: C:38-68         ------------------------------------------Exon 1.4          ------------------------------ Transcript 1 (2)
                 3fxi C  19 QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPN 158
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158

Chain D from PDB  Type:PROTEIN  Length:140
 aligned with LY96_HUMAN | Q9Y6Y9 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:140
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158
           LY96_HUMAN    19 QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKRSKGLLHIFYIPRRDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPN 158
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeeee........eeeee..........eeeeee.........eeeeeeee..ee...eeee........hhhhhh.....eeeeee..........eeeeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------G----------------------------------------------------------------------------------------------------S- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a           -----------------------------Exon 1.3  PDB: D:68-111 UniProt: 68-111     -----------------Exon 1.5b  PDB: D:129-158      Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: D:38-68         ------------------------------------------Exon 1.4          ------------------------------ Transcript 1 (2)
                 3fxi D  19 QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPN 158
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3FXI)

(no "CATH Domain" information available for 3FXI)

(no "Pfam Domain" information available for 3FXI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TLR4_HUMAN | O00206)

molecular function
	GO:0001530	lipopolysaccharide binding	Interacting selectively and non-covalently with lipopolysaccharide.
	GO:0001875	lipopolysaccharide receptor activity	Combining with a lipopolysaccharide and transmitting the signal across the cell membrane to initiate a change in cell activity. Lipopolysaccharides (LPS) are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
	GO:0002322	B cell proliferation involved in immune response	The expansion of a B cell population by cell division following B cell activation during an immune response.
	GO:0007249	I-kappaB kinase/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0007252	I-kappaB phosphorylation	The process of introducing a phosphate group into an inhibitor of kappa B (I-kappaB) protein. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing bound NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0002755	MyD88-dependent toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0002756	MyD88-independent toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor not relying on the MyD88 adaptor molecule. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0042088	T-helper 1 type immune response	An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin.
	GO:0035666	TRIF-dependent toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0002218	activation of innate immune response	Any process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species.
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0014002	astrocyte development	The process aimed at the progression of an astrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0071223	cellular response to lipoteichoic acid	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipoteichoic acid stimulus; lipoteichoic acid is a major component of the cell wall of gram-positive bacteria and typically consists of a chain of glycerol-phosphate repeating units linked to a glycolipid anchor.
	GO:0071260	cellular response to mechanical stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0016046	detection of fungus	The series of events in which a stimulus from a fungus is received and converted into a molecular signal.
	GO:0032497	detection of lipopolysaccharide	The series of events in which a lipopolysaccharide stimulus is received by a cell and converted into a molecular signal. Lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0032609	interferon-gamma production	The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
	GO:0050702	interleukin-1 beta secretion	The regulated release of interleukin 1 beta from a cell.
	GO:0060729	intestinal epithelial structure maintenance	A tissue homeostatic process required for the maintenance of the structure of the intestinal epithelium.
	GO:0031663	lipopolysaccharide-mediated signaling pathway	A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
	GO:0042116	macrophage activation	A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
	GO:0070266	necroptotic process	A programmed necrotic cell death process which begins when a cell receives a signal (e.g. a ligand binding to a death receptor or to a Toll-like receptor), and proceeds through a series of biochemical events (signaling pathways), characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3) and by critical dependence on mixed lineage kinase domain-like (MLKL), and which typically lead to common morphological features of necrotic cell death. The process ends when the cell has died. The process is divided into a signaling phase, and an execution phase, which is triggered by the former.
	GO:0070373	negative regulation of ERK1 and ERK2 cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0034128	negative regulation of MyD88-independent toll-like receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate, or extent of MyD88-independent toll-like receptor signaling pathway.
	GO:0032689	negative regulation of interferon-gamma production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032700	negative regulation of interleukin-17 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
	GO:0032707	negative regulation of interleukin-23 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-23 production.
	GO:0032715	negative regulation of interleukin-6 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
	GO:0045671	negative regulation of osteoclast differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation.
	GO:0032720	negative regulation of tumor necrosis factor production	Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
	GO:0002537	nitric oxide production involved in inflammatory response	The synthesis or release of nitric oxide following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
	GO:0030890	positive regulation of B cell proliferation	Any process that activates or increases the rate or extent of B cell proliferation.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0046330	positive regulation of JNK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0045348	positive regulation of MHC class II biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II.
	GO:0042346	positive regulation of NF-kappaB import into nucleus	Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:1900227	positive regulation of NLRP3 inflammasome complex assembly	Any process that activates or increases the frequency, rate or extent of NLRP3 inflammasome complex assembly.
	GO:0032722	positive regulation of chemokine production	Any process that activates or increases the frequency, rate, or extent of chemokine production.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0032727	positive regulation of interferon-alpha production	Any process that activates or increases the frequency, rate, or extent of interferon-alpha production.
	GO:0045359	positive regulation of interferon-beta biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-beta.
	GO:0032728	positive regulation of interferon-beta production	Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
	GO:0032729	positive regulation of interferon-gamma production	Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032732	positive regulation of interleukin-1 production	Any process that activates or increases the frequency, rate, or extent of interleukin-1 production.
	GO:0032733	positive regulation of interleukin-10 production	Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
	GO:0045084	positive regulation of interleukin-12 biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-12.
	GO:0032735	positive regulation of interleukin-12 production	Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
	GO:0032755	positive regulation of interleukin-6 production	Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
	GO:0045416	positive regulation of interleukin-8 biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-8.
	GO:0032757	positive regulation of interleukin-8 production	Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
	GO:0050671	positive regulation of lymphocyte proliferation	Any process that activates or increases the rate or extent of lymphocyte proliferation.
	GO:0060907	positive regulation of macrophage cytokine production	Any process that increases the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0045429	positive regulation of nitric oxide biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
	GO:0051770	positive regulation of nitric-oxide synthase biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
	GO:0070430	positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway	Any process that activates or increases the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 1 (NOD1) pathway.
	GO:0070434	positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway	Any process that activates or increases the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 2 (NOD2) pathway.
	GO:0010572	positive regulation of platelet activation	Any process that increases the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue.
	GO:0032874	positive regulation of stress-activated MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0042535	positive regulation of tumor necrosis factor biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
	GO:0032760	positive regulation of tumor necrosis factor production	Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
	GO:0050707	regulation of cytokine secretion	Any process that modulates the frequency, rate or extent of the regulated release of cytokines from a cell.
	GO:0002730	regulation of dendritic cell cytokine production	Any process that modulates the frequency, rate, or extent of dendritic cell cytokine production.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	GO:0009617	response to bacterium	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0034142	toll-like receptor 4 signaling pathway	Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
	GO:0002224	toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031226	intrinsic component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
	GO:0046696	lipopolysaccharide receptor complex	A multiprotein complex that consists of at least three proteins, CD14, TLR4, and MD-2, each of which is glycosylated and which functions as a lipopolysaccharide (LPS) receptor that primes the innate immune response against bacterial pathogens.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D (LY96_HUMAN | Q9Y6Y9)

molecular function
	GO:0015026	coreceptor activity	Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
	GO:0001875	lipopolysaccharide receptor activity	Combining with a lipopolysaccharide and transmitting the signal across the cell membrane to initiate a change in cell activity. Lipopolysaccharides (LPS) are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007249	I-kappaB kinase/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0002755	MyD88-dependent toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0002756	MyD88-independent toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor not relying on the MyD88 adaptor molecule. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0035666	TRIF-dependent toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0006968	cellular defense response	A defense response that is mediated by cells.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0032497	detection of lipopolysaccharide	The series of events in which a lipopolysaccharide stimulus is received by a cell and converted into a molecular signal. Lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0031663	lipopolysaccharide-mediated signaling pathway	A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
	GO:0070266	necroptotic process	A programmed necrotic cell death process which begins when a cell receives a signal (e.g. a ligand binding to a death receptor or to a Toll-like receptor), and proceeds through a series of biochemical events (signaling pathways), characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3) and by critical dependence on mixed lineage kinase domain-like (MLKL), and which typically lead to common morphological features of necrotic cell death. The process ends when the cell has died. The process is divided into a signaling phase, and an execution phase, which is triggered by the former.
	GO:0034128	negative regulation of MyD88-independent toll-like receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate, or extent of MyD88-independent toll-like receptor signaling pathway.
	GO:0031666	positive regulation of lipopolysaccharide-mediated signaling pathway	Any process that activates or increases the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
	GO:0032760	positive regulation of tumor necrosis factor production	Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0034142	toll-like receptor 4 signaling pathway	Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
cellular component
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0031226	intrinsic component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
	GO:0046696	lipopolysaccharide receptor complex	A multiprotein complex that consists of at least three proteins, CD14, TLR4, and MD-2, each of which is glycosylated and which functions as a lipopolysaccharide (LPS) receptor that primes the innate immune response against bacterial pathogens.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	Cis Peptide Bonds
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	3fxi
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(no "Related Entries Specified in the PDB File" available for 3FXI)

Description

Compounds

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Ligands, Modified Residues, Ions (10, 52)

Sites (52, 52)

SS Bonds (16, 16)

Cis Peptide Bonds (4, 4)

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