4QBZ - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN TLR8 IN COMPLEX WITH DS-802

Authors :   H. Tanji, U. Ohto, T. Shimizu

Date :   09 May 14 (Deposition) - 22 Oct 14 (Release) - 22 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Leucine Rich Repeat, Glycosylation, Innate Immunity, Rna Recognition, Ssrna, Rna Binding, Secreted, Structure-Based Ligand Design, Tlr8 And Tlr7 Agonist, Vaccine Adjuvants, Rna Receptor, Antiviral And Antitumor Drug Binding, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Yoo, D. B. Salunke, D. Sil, X. Guo, A. C. D. Salyer, A. R. Hermanson, M. Kumar, S. S. Malladi, R. Balakrishna, W. H. Thompson, H. Tanji, U. Ohto, T. Shimizu, S. A. David
Determinants Of Activity At Human Toll-Like Receptors 7 And 8: Quantitative Structure-Activity Relationship (Qsar) Of Diverse Heterocyclic Scaffolds
J. Med. Chem. V. 57 7955 2014
PubMed-ID: 25192394 | Reference-DOI: 10.1021/JM500744F

Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 8
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell	:	DROSOPHILA S2
	Expression System Common	:	FRUIT FLY
	Expression System Taxid	:	7227
	Fragment	:	UNP RESIDUES 27-827
	Gene	:	TLR8
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TLR8

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 32)

Asymmetric/Biological Unit (4, 32)

No.	Name	Count	Type	Full Name
1	BMA	5	Ligand/Ion	BETA-D-MANNOSE
2	D80	2	Ligand/Ion	2-BUTYL[1,3]OXAZOLO[4,5-C]QUINOLIN-4-AMINE
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	23	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Sites (19, 19)

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:543 , ASP A:545 , GLY A:572 , VAL A:573 , THR A:574 , TYR B:348 , GLY B:376 , ILE B:403 , PHE B:405 , ARG B:429	BINDING SITE FOR RESIDUE D80 A 917
02	AC2	SOFTWARE	PHE A:346 , TYR A:348 , GLY A:376 , VAL A:378 , PHE A:405 , ARG A:429 , ASP B:543 , ASP B:545 , GLY B:572 , VAL B:573 , THR B:574 , HOH B:1115	BINDING SITE FOR RESIDUE D80 B 901
03	AC3	SOFTWARE	ASN A:80 , ASN A:123	BINDING SITE FOR MONO-SACCHARIDE NAG A 901 BOUND TO ASN A 80
04	AC4	SOFTWARE	LYS A:226 , PHE A:228 , SER A:230 , LEU A:250 , ASP A:252 , SER A:254 , ASN A:293 , ASP A:462 , HIS A:464 , SER A:465 , ASN A:466 , PHE A:467 , HOH A:1050 , HOH A:1189 , HOH A:1260	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 293 RESIDUES 902 TO 906
05	AC5	SOFTWARE	LEU A:367 , SER A:368 , ARG A:370 , ASN A:395 , TYR B:482 , GLY B:483 , ASP B:506 , ALA B:508 , LYS B:533 , HOH B:1112	BINDING SITE FOR MONO-SACCHARIDE NAG A 907 BOUND TO ASN A 395
06	AC6	SOFTWARE	LYS A:476 , SER A:489 , LEU A:490 , ASN A:511 , ASP A:536 , HOH A:1047	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 511 RESIDUES 908 TO 909
07	AC7	SOFTWARE	SER A:522 , ASN A:546 , HOH A:1203	BINDING SITE FOR MONO-SACCHARIDE NAG A 910 BOUND TO ASN A 546
08	AC8	SOFTWARE	THR A:551 , ASN A:582	BINDING SITE FOR MONO-SACCHARIDE NAG A 911 BOUND TO ASN A 582
09	AC9	SOFTWARE	LYS A:476 , GLN A:478 , TYR A:534 , ASP A:560 , ASN A:590 , GLU A:612 , VAL A:614 , HOH A:1077 , HOH A:1104 , HOH A:1140 , HOH A:1159 , HOH A:1246	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 590 RESIDUES 912 TO 914
10	BC1	SOFTWARE	LYS A:608 , SER A:609 , VAL A:611 , ASN A:640 , HOH A:1148 , GLN B:288 , ARG B:290	BINDING SITE FOR MONO-SACCHARIDE NAG A 915 BOUND TO ASN A 640
11	BC2	SOFTWARE	ASN A:656 , PHE A:678 , ASN A:680 , THR A:682 , LEU A:683	BINDING SITE FOR MONO-SACCHARIDE NAG A 916 BOUND TO ASN A 680
12	BC3	SOFTWARE	LYS B:226 , PHE B:228 , SER B:230 , LEU B:250 , ASP B:252 , SER B:254 , TYR B:291 , ASN B:293 , ASP B:462 , HIS B:464 , SER B:465 , ASN B:466 , PHE B:467 , HOH B:1086 , HOH B:1221	BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 293 RESIDUES 902 TO 905
13	BC4	SOFTWARE	TYR A:482 , GLY A:483 , ALA A:508 , LYS A:533 , HOH A:1130 , HOH A:1254 , LEU B:367 , SER B:368 , ARG B:370 , ASN B:395	BINDING SITE FOR MONO-SACCHARIDE NAG B 906 BOUND TO ASN B 395
14	BC5	SOFTWARE	LYS B:476 , SER B:489 , LEU B:490 , ASN B:511 , ASP B:536 , HOH B:1036 , HOH B:1053 , HOH B:1209	BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 511 RESIDUES 907 TO 908
15	BC6	SOFTWARE	ASP B:118 , SER B:522 , ASN B:546 , HOH B:1045 , HOH B:1190	BINDING SITE FOR MONO-SACCHARIDE NAG B 909 BOUND TO ASN B 546
16	BC7	SOFTWARE	GLN B:581 , ASN B:582	BINDING SITE FOR MONO-SACCHARIDE NAG B 910 BOUND TO ASN B 582
17	BC8	SOFTWARE	LYS B:476 , GLN B:478 , TYR B:534 , ASP B:560 , SER B:562 , VAL B:588 , ASN B:590 , GLU B:612 , HOH B:1047 , HOH B:1093 , HOH B:1135 , HOH B:1153 , HOH B:1159	BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 590 RESIDUES 911 TO 913
18	BC9	SOFTWARE	GLN A:288 , ARG A:290 , LYS B:608 , SER B:609 , VAL B:611 , ASN B:640 , HOH B:1098 , HOH B:1218	BINDING SITE FOR MONO-SACCHARIDE NAG B 914 BOUND TO ASN B 640
19	CC1	SOFTWARE	ASN B:656 , ASN B:680 , THR B:682 , LEU B:683	BINDING SITE FOR MONO-SACCHARIDE NAG B 915 BOUND TO ASN B 680

SS Bonds (12, 12)

Asymmetric/Biological Unit

No.	Residues
1	A:36	-	A:49
2	A:181	-	A:187
3	A:257	-	A:270
4	A:260	-	A:267
5	A:479	-	A:509
6	A:776	-	A:803
7	B:36	-	B:49
8	B:181	-	B:187
9	B:257	-	B:270
10	B:260	-	B:267
11	B:479	-	B:509
12	B:776	-	B:803

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:754
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eee..................eee.......ee............eee.........ee............eee..................eee.......eehhhhhh......eee..............ee............eee..................eee.......ee............eee.................hhhhh..ee............eee.........hhhhhh......eee.....hhhhhhhhhhhhhh....eee................hhhhhhh....eee.......eehhhhhhhhh......eee.......ee.hhhhhhh....eee.............................hhhhhh...eee.....................eee......................eee.....................eee...hhhhhh.......hhhhhhh....eee.....................eee....hhhhhh..................eee.........hhhhhhh......eee.........hhhhhhhh....eee...........hhhhh.....eee.....................eee.........hhhhhh........eee.....ee.hhhhhhhhhhhhhh......hhhhh.eee.......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qbz A  31 SRSYPCDEKKQNDSVIAECSNRRLQEVPQTVGKYVTELDLSDNFITHITNESFQGLQNLTKINLNHNPNVGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPESLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCEKTNIEDGVFETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLINLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSSTSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSFNYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNLSTINLGINFIKQIDFKLFQNFSNLEIIYLSENRISPLVTDFEFDPHSNFYHFTRPLIKPQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQVLSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRIAGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRLDILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELHINDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLSHNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSALETKTTTKLSMLELHGNPFECTCDIGDFRRWMDEHLNVKIPRLVDVICASPGDQRGKSIVSLE 818
                                    40        50        60        70        80        90       100|      122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432 ||    464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814    
                                                                                               100|                                                                                                                                                                                                                                                                                                                              434|                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                113                                                                                                                                                                                                                                                                                                                               457

Chain B from PDB  Type:PROTEIN  Length:751
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee...eee..................eee.......ee............eee...........ee............eee..................eee.......eehhhhhh......eee..............ee............eee..................eee.......ee............eee.................hhhhh..ee............eee.........hhhhhh......eee.....hhhhhhhhhhhhhh....eee................hhhhhhh....eee.......eehhhhhhhhh......eee.......ee.hhhhhhh....eee...........................hhhhhh...eee.....................eee......................eee.....................eee...hhhhhh.......hhhhhhh....eee.....................eee....hhhhhh..................eee.........hhhhhhh......eee.........hhhhhhhh....eee...........hhhhh.....eee...........hhhhh.....eee.........hhhhhh........eee.....ee.hhhhhhhhhhhhhh......hhhhh.eee.......hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qbz B  31 SRSYPCDEKKQVIAECSNRRLQEVPQTVGKYVTELDLSDNFITHITNESFQGLQNLTKINLNHNPNVQNGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPESLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCEKTNIEDGVFETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLINLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSSTSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSFNYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNLSTINLGINFIKQIDFKLFQNFSNLEIIYLSENRISPLVFEFDPHSNFYHFTRPLIKPQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQVLSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRIAGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRLDILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELHINDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLSHNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSALETKTTTKLSMLELHGNPFECTCDIGDFRRWMDEHLNVKIPRLVDVICASPGDQRGKSIVSLE 818
                                    40||      53        63        73        83        93       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433||     467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817 
                                     41|                                                     101|                                                                                                                                                                                                                                                                                                                               434|                                                                                                                                                                                                                                                                                                                                                                       
                                      45                                                      112                                                                                                                                                                                                                                                                                                                                459

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (33, 33)

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	Cis Peptide Bonds
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		Ser A:805 - Pro A:806	[ RasMol ]
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