1ZA3 - JenaLib

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Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF THE YSD1 FAB BOUND TO DR5

Authors :   F. A. Fellouse, B. Li, D. M. Compaan, A. A. Peden, S. G. Hymowitz, S. S. Sid

Date :   05 Apr 05 (Deposition) - 14 Jun 05 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.35

Chains :   Asym. Unit : A,B,H,L,R,S
Biol. Unit 1: A,B,S  (1x)
Biol. Unit 2: H,L,R  (1x)

Keywords :   Phage Display, Protein Engineering, Combinatorial Mutagenesis, Antibody Library, Death Receptor-5, Immune System-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. A. Fellouse, B. Li, D. M. Compaan, A. A. Peden, S. G. Hymowitz, S. S. Sidhu
Molecular Recognition By A Binary Code.
J. Mol. Biol. V. 348 1153 2005
PubMed-ID: 15854651 | Reference-DOI: 10.1016/J.JMB.2005.03.041

Molecule 1 - FAB-YSD1 LIGHT CHAIN
	Chains	:	A, L
	Engineered	:	YES
	Fragment	:	FAB LIGHT CHAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB-YSD1 HEAVY CHAIN
	Chains	:	B, H
	Engineered	:	YES
	Fragment	:	FAB HEAVY CHAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 10B
	Chains	:	R, S
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PACGP67-B
	Expression System Strain	:	HI5
	Expression System Taxid	:	7108
	Expression System Vector Type	:	VIRUS
	Fragment	:	EXTRA-CELLULAR DOMAIN
	Gene	:	DR5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DEATH RECEPTOR 5, TNF-RELATED APOPTOSIS-INDUCING LIGAND RECEPTOR 2, TRAIL RECEPTOR-2, TRAIL-R2, DR5

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	H	L	R	S
Biological Unit 1 (1x)	:	A	B				S
Biological Unit 2 (1x)	:			H	L	R

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ZA3)

(no "Site" information available for 1ZA3)

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:133	-	A:193
3	B:22	-	B:92
4	B:140	-	B:196
5	H:22	-	H:92
6	H:140	-	H:196
7	L:23	-	L:88
8	L:133	-	L:193
9	R:28	-	R:41
10	R:44	-	R:60
11	R:63	-	R:76
12	R:66	-	R:84
13	R:86	-	R:100
14	R:103	-	R:117
15	S:28	-	S:41
16	S:44	-	S:60
17	S:63	-	S:76
18	S:66	-	S:84
19	S:86	-	S:100
20	S:103	-	S:117
21	S:107	-	S:125

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Tyr A:139	-	Pro A:140
3	Phe B:146	-	Pro B:147
4	Glu B:148	-	Pro B:149
5	Ser L:7	-	Pro L:8
6	Tyr L:139	-	Pro L:140
7	Phe H:146	-	Pro H:147
8	Glu H:148	-	Pro H:149

(no "SAP(SNP)/Variant" information available for 1ZA3)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNFR_NGFR_2	PS50050	TNFR/NGFR family cysteine-rich region domain profile.	TR10B_HUMAN	96-137 138-178	4	R:43-84 S:43-84 R:85-123 S:85-125
2	TNFR_NGFR_1	PS00652	TNFR/NGFR family cysteine-rich region signature.	TR10B_HUMAN	97-137 137-178	4	R:44-84 S:44-84 R:84-123 S:84-125

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNFR_NGFR_2	PS50050	TNFR/NGFR family cysteine-rich region domain profile.	TR10B_HUMAN	96-137 138-178	2	- S:43-84 - S:85-125
2	TNFR_NGFR_1	PS00652	TNFR/NGFR family cysteine-rich region signature.	TR10B_HUMAN	97-137 137-178	2	- S:44-84 - S:84-125

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNFR_NGFR_2	PS50050	TNFR/NGFR family cysteine-rich region domain profile.	TR10B_HUMAN	96-137 138-178	2	R:43-84 - R:85-123 -
2	TNFR_NGFR_1	PS00652	TNFR/NGFR family cysteine-rich region signature.	TR10B_HUMAN	97-137 137-178	2	R:44-84 - R:84-123 -

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000276431	1a	ENSE00001335538	chr8:22926692-22926264	429	TR10B_HUMAN	1-48	48	0	-	-
1.3a	ENST00000276431	3a	ENSE00001232611	chr8:22900756-22900651	106	TR10B_HUMAN	49-84	36	2	R:21-31 S:21-31	11 11
1.4	ENST00000276431	4	ENSE00000980145	chr8:22888385-22888272	114	TR10B_HUMAN	84-122	39	2	R:31-69 S:31-69	39 39
1.5	ENST00000276431	5	ENSE00000980146	chr8:22887234-22887123	112	TR10B_HUMAN	122-159	38	2	R:69-103 S:69-106	35 38
1.6c	ENST00000276431	6c	ENSE00001203553	chr8:22886115-22885844	272	TR10B_HUMAN	159-250	92	2	R:116-123 S:106-126	8 21
1.7b	ENST00000276431	7b	ENSE00000980148	chr8:22885266-22885235	32	TR10B_HUMAN	250-260	11	0	-	-
1.8b	ENST00000276431	8b	ENSE00001232589	chr8:22884801-22884646	156	TR10B_HUMAN	261-312	52	0	-	-
1.9	ENST00000276431	9	ENSE00001689788	chr8:22881773-22881701	73	TR10B_HUMAN	313-337	25	0	-	-
1.10d	ENST00000276431	10d	ENSE00002120034	chr8:22880497-22877646	2852	TR10B_HUMAN	337-440	104	0	-	-

Asymmetric 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:213
                                                                                                                                                                                                                                                      
               SCOP domains d1za3a1 A:1-106 Immunoglobulin light chain kappa variable domain, VL-kappa                                d1za3a2 A:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1za3A01 A:1-107 Immunoglobulins                                                                            1za3A02 A:108-213 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......ee......eeeeee...hhhhheeeeeee..........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1za3 A    1 DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYAASYLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQSSSSPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains d1za3b1 B:1-113 Camelid IG heavy chain variable domain, VHh                                                                      d1za3b2 B:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1za3B01 B:1-113 Immunoglobulins                                                                                                  1za3B02 B:114-214 Immunoglobulins                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee..hhhhhhhh......eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1za3 B    1 EVQLVESGGGLVQPGGSLRLSCAASGFSIYSYSIHWVRQAPGKGLEWVASISPYSGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRYSSYYSYYYSSSSYSYAMDYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||| 104       114       124  ||   140       150       160       170       180       190       200       210    
                                                                              52A                            82A||               100A|||||100J||                        127|                                                                                
                                                                                                              82B|                100B|||||100K|                         134                                                                                
                                                                                                               82C                 100C|||||100L                                                                                                            
                                                                                                                                    100D|||||                                                                                                               
                                                                                                                                     100E||||                                                                                                               
                                                                                                                                      100F|||                                                                                                               
                                                                                                                                       100G||                                                                                                               
                                                                                                                                        100H|                                                                                                               
                                                                                                                                         100I

Chain H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains d1za3h1 H:1-113 Camelid IG heavy chain variable domain, VHh                                                                      d1za3h2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1za3H01 H:1-113 Immunoglobulins                                                                                                  1za3H02 H:114-214 Immunoglobulins                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee.......eeeeee....eeeeee........eeeeeeee..hhhhhhhh......eeee...eeeee........eeeee.....eeeeeeeeee....eeeee.hhh....eee..........eeeeeeeeehhhhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1za3 H    1 EVQLVESGGGLVQPGGSLRLSCAASGFSIYSYSIHWVRQAPGKGLEWVASISPYSGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRYSSYYSYYYSSSSYSYAMDYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||| 104       114       124  ||   140       150       160       170       180       190       200       210    
                                                                              52A                            82A||               100A|||||100J||                        127|                                                                                
                                                                                                              82B|                100B|||||100K|                         134                                                                                
                                                                                                               82C                 100C|||||100L                                                                                                            
                                                                                                                                    100D|||||                                                                                                               
                                                                                                                                     100E||||                                                                                                               
                                                                                                                                      100F|||                                                                                                               
                                                                                                                                       100G||                                                                                                               
                                                                                                                                        100H|                                                                                                               
                                                                                                                                         100I

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1za3l1 L:1-106 Immunoglobulin light chain kappa variable domain, VL-kappa                                d1za3l2 L:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1za3L01 L:1-107 Immunoglobulins                                                                            1za3L02 L:108-213 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eee.....eeeeee...hhhhh.eeeeee..........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.........ee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeee..........eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1za3 L    1 DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYAASYLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQSSSSPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain R from PDB  Type:PROTEIN  Length:91
 aligned with TR10B_HUMAN | O14763 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:103
                                    83        93       103       113       123       133       143       153       163       173   
         TR10B_HUMAN     74 SSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDI  176
               SCOP domains d1za3r1 R:21-61                          d1za3r2 R:62-101                        d1            za3r3 R: SCOP domains
               CATH domains 1za3R01 R:21-61                          1za3R02 R:62-101                        ---------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....eee......eee.....ee..........ee........eeee........eee....eeee..eeeeeee.------------........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------TNFR_NGFR_2  PDB: R:43-84 UniProt: 96-137 TNFR_NGFR_2  PDB: R:85-123              PROSITE (1)
                PROSITE (2) -----------------------TNFR_NGFR_1  PDB: R:44-84 UniProt: 97-137--------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------TNFR_NGFR_1  PDB: R:84-123               PROSITE (3)
           Transcript 1 (1) Exon 1.3a  -------------------------------------Exon 1.5  PDB: R:69-103 [INCOMPLETE]  ----------------- Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.4  PDB: R:31-69 UniProt: 84-122 ------------------------------------Exon 1.6c          Transcript 1 (2)
                1za3 R   21 SSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKC------------DCTPWSDI  123
                                    30        40        50        60        70        80        90       100  |      -     | 120   
                                                                                                            103          116

Chain S from PDB  Type:PROTEIN  Length:106
 aligned with TR10B_HUMAN | O14763 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:106
                                    83        93       103       113       123       133       143       153       163       173      
         TR10B_HUMAN     74 SSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECV  179
               SCOP domains d1za3s1 S:21-61                          d1za3s2 S:62-101                        d1za3s3 S:102-123     --- SCOP domains
               CATH domains 1za3S01 S:21-61                          1za3S02 S:62-101                        ------------------------- CATH domains
           Pfam domains (1) -----------------------TNFR_c6-1za3S01 S:44-84                  ------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------TNFR_c6-1za3S02 S:44-84                  ------------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhh....eee......eee.....ee..........ee.......eeeee........eeee...eeee..eeeeeee.........eeee........eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------TNFR_NGFR_2  PDB: S:43-84 UniProt: 96-137 TNFR_NGFR_2  PDB: S:85-125               - PROSITE (1)
                PROSITE (2) -----------------------TNFR_NGFR_1  PDB: S:44-84 UniProt: 97-137------------------------------------------ PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------TNFR_NGFR_1  PDB: S:84-125                - PROSITE (3)
           Transcript 1 (1) Exon 1.3a  -------------------------------------Exon 1.5  PDB: S:69-106               -------------------- Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.4  PDB: S:31-69 UniProt: 84-122 ------------------------------------Exon 1.6c             Transcript 1 (2)
                1za3 S   21 SSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECV  126
                                    30        40        50        60        70        80        90       100       110       120

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Tumor Necrosis Factor Receptor, subunit A; domain 2 (17)

Homologous Superfamily: Tumor Necrosis Factor Receptor, subunit A, domain 2 (16)

[unclassified] (1)

1a	1za3R02	R:62-101
1b	1za3S02	S:62-101
1c	1za3R01	R:21-61
1d	1za3S01	S:21-61

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

[unclassified] (54)

2a	1za3A02	A:108-213
2b	1za3B02	B:114-214
2c	1za3H02	H:114-214
2d	1za3B01	B:1-113
2e	1za3H01	H:1-113
2f	1za3L02	L:108-213
2g	1za3A01	A:1-107
2h	1za3L01	L:1-107

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: TNFR_c6] (13)

Family: TNFR_c6 (13)

Homo sapiens (Human) (8)

1a	TNFR_c6-1za3S01	S:44-84
1b	TNFR_c6-1za3S02	S:44-84

Asymmetric Unit(hide GO term definitions)

Chain R,S (TR10B_HUMAN | O14763)

molecular function
	GO:0045569	TRAIL binding	Interacting selectively and non-covalently with TRAIL (TNF-related apoptosis inducing ligand), a member of the tumor necrosis factor ligand family that rapidly induces apoptosis in a variety of transformed cell lines.
	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:0005031	tumor necrosis factor-activated receptor activity	Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
biological process
	GO:0007250	activation of NF-kappaB-inducing kinase activity	The stimulation of the activity of NF-kappaB-inducing kinase through phosphorylation at specific residues.
	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
	GO:0097296	activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway	Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the apoptotic signaling pathway.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	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: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:0008625	extrinsic apoptotic signaling pathway via death domain receptors	A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered.
	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: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:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:1902042	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
	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:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:1902041	regulation of extrinsic apoptotic signaling pathway via death domain receptors	Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
	GO:0034976	response to endoplasmic reticulum stress	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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
	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:0033209	tumor necrosis factor-mediated signaling pathway	A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
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	1za3
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UniProtKB/Swiss-Prot
	TR10B_HUMAN \| O14763	:	1d0g 1d4v 1du3 2h9g 3x3f 4i9x 4n90 4od2

1d0g	THE CRYSTAL STRUCTURE OF HDR5 BOUND TO APO2L/TRAIL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (21, 21)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (4, 8)

Sequences/Alignments

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SCOP Domains (5, 14)

CATH Domains (2, 12)

Pfam Domains (1, 2)

Gene Ontology (30, 30)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File