4HY0 - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF XIAP BIR3 WITH T3256336

Authors :   G. S. Snell, D. R. Dougan

Date :   12 Nov 12 (Deposition) - 30 Jan 13 (Release) - 07 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.84

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,H  (1x)
Biol. Unit 3: D,E  (1x)
Biol. Unit 4: F,G  (1x)

Keywords :   Bir3, Baculoviral Iap Repeat-Containing Protein 4, Apoptotic Suppressor. Inhibitor Of Caspase-3, -7 And -9. , Interacts With Smac And With Prss25, Xiap, Birc4, X-Linked Inhibitor Of Apoptosis, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Hashimoto, B. Saito, N. Miyamoto, Y. Oguro, D. Tomita, Z. Shiokawa, M. Asano, H. Kakei, N. Taya, M. Kawasaki, H. Sumi, M. Yabuki, K. Iwai, S. Yoshida, M. Yoshimatsu, K. Aoyama, Y. Kosugi, T. Kojima, N. Morishita, D. R. Dougan, G. P. Snell, S. Imamura, T. Ishikawa
Design And Synthesis Of Potent Inhibitor Of Apoptosis (Iap) Proteins Antagonists Bearing An Octahydropyrrolo[1, 2-A]Pyrazine Scaffold As A Novel Proline Mimetic.
J. Med. Chem. V. 56 1228 2013
PubMed-ID: 23298277 | Reference-DOI: 10.1021/JM301674Z

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE XIAP
	Chains	:	A, B, C, D, E, F, G, H
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	API3, BIRC4, IAP3, XIAP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4, IAP-LIKE PROTEIN, ILP, HILP, INHIBITOR OF APOPTOSIS PROTEIN 3, IAP-3, HIAP-3, HIAP3, X-LINKED INHIBITOR OF APOPTOSIS PROTEIN, X-LINKED IAP

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C					H
Biological Unit 3 (1x)	:				D	E
Biological Unit 4 (1x)	:						F	G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 22)

No.	Name	Count	Type	Full Name
1	1AQ	8	Ligand/Ion	(3S,7R,8AR)-2-{(2S)-2-(4,4-DIFLUOROCYCLOHEXYL)-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-N-[(4R)-3,4-DIHYDRO-2H-CHROMEN-4-YL]-7-ETHOXYOCTAHYDROPYRROLO[1,2-A]PYRAZINE-3-CARBOXAMIDE
2	ZN	14	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	1AQ	2	Ligand/Ion	(3S,7R,8AR)-2-{(2S)-2-(4,4-DIFLUOROCYCLOHEXYL)-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-N-[(4R)-3,4-DIHYDRO-2H-CHROMEN-4-YL]-7-ETHOXYOCTAHYDROPYRROLO[1,2-A]PYRAZINE-3-CARBOXAMIDE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	1AQ	2	Ligand/Ion	(3S,7R,8AR)-2-{(2S)-2-(4,4-DIFLUOROCYCLOHEXYL)-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-N-[(4R)-3,4-DIHYDRO-2H-CHROMEN-4-YL]-7-ETHOXYOCTAHYDROPYRROLO[1,2-A]PYRAZINE-3-CARBOXAMIDE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	1AQ	2	Ligand/Ion	(3S,7R,8AR)-2-{(2S)-2-(4,4-DIFLUOROCYCLOHEXYL)-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-N-[(4R)-3,4-DIHYDRO-2H-CHROMEN-4-YL]-7-ETHOXYOCTAHYDROPYRROLO[1,2-A]PYRAZINE-3-CARBOXAMIDE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	1AQ	2	Ligand/Ion	(3S,7R,8AR)-2-{(2S)-2-(4,4-DIFLUOROCYCLOHEXYL)-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-N-[(4R)-3,4-DIHYDRO-2H-CHROMEN-4-YL]-7-ETHOXYOCTAHYDROPYRROLO[1,2-A]PYRAZINE-3-CARBOXAMIDE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:300 , CYS A:303 , HIS A:320 , CYS A:327	BINDING SITE FOR RESIDUE ZN A 401
02	AC2	SOFTWARE	LYS A:322 , HIS A:343 , HIS A:346 , HIS B:343	BINDING SITE FOR RESIDUE ZN A 402
03	AC3	SOFTWARE	LYS A:297 , GLY A:306 , LEU A:307 , THR A:308 , ASP A:309 , GLU A:314 , GLN A:319 , TRP A:323 , TYR A:324 , LEU B:348 , THR D:345 , LEU D:348 , GLU D:349	BINDING SITE FOR RESIDUE 1AQ A 403
04	AC4	SOFTWARE	CYS B:300 , CYS B:303 , HIS B:320 , CYS B:327	BINDING SITE FOR RESIDUE ZN B 401
05	AC5	SOFTWARE	HIS A:343 , LYS B:322 , HIS B:343 , HIS B:346	BINDING SITE FOR RESIDUE ZN B 402
06	AC6	SOFTWARE	LEU A:344 , LYS B:297 , GLY B:306 , LEU B:307 , THR B:308 , ASP B:309 , GLU B:314 , GLN B:319 , TRP B:323 , TYR B:324 , THR G:345 , LEU G:348 , GLU G:349	BINDING SITE FOR RESIDUE 1AQ B 403
07	AC7	SOFTWARE	CYS C:300 , CYS C:303 , HIS C:320 , CYS C:327	BINDING SITE FOR RESIDUE ZN C 401
08	AC8	SOFTWARE	LYS C:297 , GLY C:306 , LEU C:307 , THR C:308 , ASP C:309 , LYS C:311 , GLU C:314 , GLN C:319 , TRP C:323 , TYR C:324 , THR F:345 , LEU H:344	BINDING SITE FOR RESIDUE 1AQ C 402
09	AC9	SOFTWARE	CYS D:300 , CYS D:303 , HIS D:320 , CYS D:327	BINDING SITE FOR RESIDUE ZN D 401
10	BC1	SOFTWARE	LYS D:322 , HIS D:343 , HIS D:346 , HIS E:343	BINDING SITE FOR RESIDUE ZN D 402
11	BC2	SOFTWARE	THR C:345 , HIS C:346 , GLU C:349 , GLY D:306 , LEU D:307 , THR D:308 , ASP D:309 , GLU D:314 , TRP D:323 , TYR D:324 , HOH D:501	BINDING SITE FOR RESIDUE 1AQ D 403
12	BC3	SOFTWARE	CYS E:300 , CYS E:303 , HIS E:320 , CYS E:327	BINDING SITE FOR RESIDUE ZN E 401
13	BC4	SOFTWARE	HIS D:343 , LYS E:322 , HIS E:343 , HIS E:346	BINDING SITE FOR RESIDUE ZN E 402
14	BC5	SOFTWARE	THR B:345 , LEU B:348 , LEU E:292 , LYS E:297 , GLY E:306 , LEU E:307 , THR E:308 , ASP E:309 , GLU E:314 , GLN E:319 , TRP E:323 , TYR E:324	BINDING SITE FOR RESIDUE 1AQ E 403
15	BC6	SOFTWARE	CYS F:300 , CYS F:303 , HIS F:320 , CYS F:327	BINDING SITE FOR RESIDUE ZN F 401
16	BC7	SOFTWARE	LYS F:322 , HIS F:343 , HIS F:346 , HIS G:343	BINDING SITE FOR RESIDUE ZN F 402
17	BC8	SOFTWARE	THR A:345 , LEU A:348 , GLU A:349 , LEU F:292 , GLY F:306 , LEU F:307 , THR F:308 , ASP F:309 , GLU F:314 , GLN F:319 , TRP F:323 , TYR F:324	BINDING SITE FOR RESIDUE 1AQ F 403
18	BC9	SOFTWARE	CYS G:300 , CYS G:303 , HIS G:320 , CYS G:327	BINDING SITE FOR RESIDUE ZN G 401
19	CC1	SOFTWARE	HIS F:343 , LYS G:322 , HIS G:343 , HIS G:346	BINDING SITE FOR RESIDUE ZN G 402
20	CC2	SOFTWARE	LEU F:344 , LEU F:348 , LEU G:292 , LYS G:299 , GLY G:306 , LEU G:307 , THR G:308 , ASP G:309 , TRP G:310 , GLU G:314 , GLN G:319 , TRP G:323 , TYR G:324 , THR H:345 , LEU H:348 , GLU H:349	BINDING SITE FOR RESIDUE 1AQ G 403
21	CC3	SOFTWARE	CYS H:300 , CYS H:303 , HIS H:320 , CYS H:327	BINDING SITE FOR RESIDUE ZN H 401
22	CC4	SOFTWARE	LEU C:344 , LEU C:348 , THR E:345 , GLY H:306 , LEU H:307 , THR H:308 , ASP H:309 , GLU H:314 , GLN H:319 , TRP H:323 , TYR H:324	BINDING SITE FOR RESIDUE 1AQ H 402

(no "SS Bond" information available for 4HY0)

(no "Cis Peptide Bond" information available for 4HY0)

(no "SAP(SNP)/Variant" information available for 4HY0)

(no "PROSITE Motif" information available for 4HY0)

(no "Exon" information available for 4HY0)

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:96
                                                                                                                                
               SCOP domains d4hy0a_ A: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4hy0 A 254 TNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLE 349
                                   263       273       283       293       303       313       323       333       343

Chain B from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains d4hy0b_ B: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.......hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4hy0 B 254 TNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLE 349
                                   263       273       283       293       303       313       323       333       343

Chain C from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains d4hy0c_ C: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4hy0 C 254 TNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEE 350
                                   263       273       283       293       303       313       323       333       343

Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains d4hy0d_ D: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.......hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4hy0 D 254 TNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEEC 351
                                   263       273       283       293       303       313       323       333       343

Chain E from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains d4hy0e_ E: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4hy0 E 254 TNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLE 349
                                   263       273       283       293       303       313       323       333       343

Chain F from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains d4hy0f_ F: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4hy0 F 254 TNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLE 349
                                   263       273       283       293       303       313       323       333       343

Chain G from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains d4hy0g_ G: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4hy0 G 254 TNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEEC 351
                                   263       273       283       293       303       313       323       333       343

Chain H from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains d4hy0h_ H: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4hy0 H 254 TNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLE 349
                                   263       273       283       293       303       313       323       333       343

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

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

)

Class: Small proteins (3458)

Fold: Inhibitor of apoptosis (IAP) repeat (71)

Superfamily: Inhibitor of apoptosis (IAP) repeat (71)

Family: Inhibitor of apoptosis (IAP) repeat (70)

Protein domain: automated matches (24)

Human (Homo sapiens) [TaxId: 9606] (24)

1a	d4hy0a_	A:
1b	d4hy0b_	B:
1c	d4hy0c_	C:
1d	d4hy0d_	D:
1e	d4hy0e_	E:
1f	d4hy0f_	F:
1g	d4hy0g_	G:
1h	d4hy0h_	H:

(no "CATH Domain" information available for 4HY0)

(no "Pfam Domain" information available for 4HY0)

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	Cis Peptide Bonds
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	4hy0
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(no "Related Entries Specified in the PDB File" available for 4HY0)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 22)

Sites (22, 22)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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