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Title :   STRUCTURE OF AN ML-IAP/XIAP CHIMERA BOUND TO A PEPTIDOMIMETIC

Authors :   W. J. Fairbrother, M. C. Franklin

Date :   18 Aug 06 (Deposition) - 19 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Zinc Binding, Peptide Complex, Apoptosis Inhibition, Peptidomimetic, Small Molecule, Drug Design, Inhibitor-Apoptosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Zobel, L. Wang, E. Varfolomeev, M. C. Franklin, L. O. Elliott, H. J. Wallweber, D. C. Okawa, J. A. Flygare, D. Vucic, W. J. Fairbrother K. Deshayes
Design, Synthesis, And Biological Activity Of A Potent Smac Mimetic That Sensitizes Cancer Cells To Apoptosis By Antagonizing Iaps.
Acs Chem. Biol. V. 1 525 2006
PubMed-ID: 17168540 | Reference-DOI: 10.1021/CB600276Q
(for further references see the PDB file header)

Molecule 1 - BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	ML-IAP RESIDUES 63-172
	Gene	:	BIRC7
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	KIDNEY INHIBITOR OF APOPTOSIS PROTEIN, KIAP, MELANOMA INHIBITOR OF APOPTOSIS PROTEIN, ML-IAP, LIVIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 8)

No.	Name	Count	Type	Full Name
1	618	2	Ligand/Ion	(3R,6R,9AR)-2,2-DIMETHYL-6-[(N-METHYL-L-ALANYL)AMINO]-N-(3-METHYL-1-PHENYL-1H-PYRAZOL-5-YL)-5-OXO-2,3,5,6,9,9A-HEXAHYDRO[1,3]THIAZOLO[3,2-A]AZEPINE-3-CARBOXAMIDE
2	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	LI	1	Ligand/Ion	LITHIUM ION
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	618	1	Ligand/Ion	(3R,6R,9AR)-2,2-DIMETHYL-6-[(N-METHYL-L-ALANYL)AMINO]-N-(3-METHYL-1-PHENYL-1H-PYRAZOL-5-YL)-5-OXO-2,3,5,6,9,9A-HEXAHYDRO[1,3]THIAZOLO[3,2-A]AZEPINE-3-CARBOXAMIDE
2	BTB	-1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	LI	-1	Ligand/Ion	LITHIUM ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	618	1	Ligand/Ion	(3R,6R,9AR)-2,2-DIMETHYL-6-[(N-METHYL-L-ALANYL)AMINO]-N-(3-METHYL-1-PHENYL-1H-PYRAZOL-5-YL)-5-OXO-2,3,5,6,9,9A-HEXAHYDRO[1,3]THIAZOLO[3,2-A]AZEPINE-3-CARBOXAMIDE
2	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	LI	-1	Ligand/Ion	LITHIUM ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:124 , CYS A:127 , HIS A:144 , CYS A:151	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	CYS B:124 , CYS B:127 , HIS B:144 , CYS B:151	BINDING SITE FOR RESIDUE ZN B 1001
3	AC3	SOFTWARE	SER B:93 , ASP B:96 , HIS B:115 , EDO B:201	BINDING SITE FOR RESIDUE LI B 1002
4	AC4	SOFTWARE	LYS A:121 , VAL A:122 , ARG A:123 , GLY A:130 , LEU A:131 , GLN A:132 , SER A:133 , TRP A:134 , ASP A:138 , GLU A:143 , TRP A:147 , ARG B:136	BINDING SITE FOR RESIDUE 618 A 501
5	AC5	SOFTWARE	PRO A:104 , GLU A:106 , LEU A:107 , LYS B:121 , ARG B:123 , GLY B:130 , LEU B:131 , GLN B:132 , SER B:133 , TRP B:134 , ASP B:138 , GLU B:143 , TRP B:147 , HOH B:1054 , HOH B:1058 , HOH B:1065	BINDING SITE FOR RESIDUE 618 B 501
6	AC6	SOFTWARE	LYS B:146 , TRP B:147 , HIS B:170 , HOH B:1023 , HOH B:1036 , HOH B:1061	BINDING SITE FOR RESIDUE BTB B 301
7	AC7	SOFTWARE	SER A:93 , SER B:93 , ASP B:96 , HIS B:115 , GLY B:117 , LI B:1002	BINDING SITE FOR RESIDUE EDO B 201
8	AC8	SOFTWARE	CYS B:127 , PHE B:148 , PRO B:149 , GLY B:150	BINDING SITE FOR RESIDUE EDO B 202

(no "SS Bond" information available for 2I3I)

(no "Cis Peptide Bond" information available for 2I3I)

(no "SAP(SNP)/Variant" information available for 2I3I)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIR_REPEAT_1	PS01282	BIR repeat.	BIRC7_HUMAN	87-154	2	A:87-154 B:87-154
2	BIR_REPEAT_2	PS50143	BIR repeat profile.	BIRC7_HUMAN	90-155	2	A:90-155 B:90-155

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIR_REPEAT_1	PS01282	BIR repeat.	BIRC7_HUMAN	87-154	1	A:87-154 -
2	BIR_REPEAT_2	PS50143	BIR repeat profile.	BIRC7_HUMAN	90-155	1	A:90-155 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIR_REPEAT_1	PS01282	BIR repeat.	BIRC7_HUMAN	87-154	1	- B:87-154
2	BIR_REPEAT_2	PS50143	BIR repeat profile.	BIRC7_HUMAN	90-155	1	- B:90-155

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000217169	1	ENSE00001386758	chr20:61867235-61867797	563	BIRC7_HUMAN	1-117	117	2	A:78-117 B:78-117	40 40
1.2	ENST00000217169	2	ENSE00000856558	chr20:61869255-61869354	100	BIRC7_HUMAN	117-150	34	2	A:117-150 B:117-150	34 34
1.3c	ENST00000217169	3c	ENSE00000663365	chr20:61869748-61869829	82	BIRC7_HUMAN	150-177	28	2	A:150-167 B:150-172	18 23
1.4	ENST00000217169	4	ENSE00000663366	chr20:61869921-61869966	46	BIRC7_HUMAN	178-193	16	0	-	-
1.5	ENST00000217169	5	ENSE00000856559	chr20:61870514-61870585	72	BIRC7_HUMAN	193-217	25	0	-	-
1.6a	ENST00000217169	6a	ENSE00001174107	chr20:61870710-61870962	253	BIRC7_HUMAN	217-298	82	0	-	-
1.7c	ENST00000217169	7c	ENSE00001816361	chr20:61871608-61871859	252	BIRC7_HUMAN	-	0	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
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Chain A from PDB  Type:PROTEIN  Length:90
 aligned with BIRC7_HUMAN | Q96CA5 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:90
                                    87        97       107       117       127       137       147       157       167
          BIRC7_HUMAN    78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPSCQFLLRSKGRDFVHSVQ 167
               SCOP domains d2i3ia_ A: BIR-containing protein 7 (ML-IAP, livin)                                        SCOP domains
               CATH domains 2i3iA00 A:78-167 Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------BIR_REPEAT_1  PDB: A:87-154 UniProt: 87-154                         ------------- PROSITE (1)
                PROSITE (2) ------------BIR_REPEAT_2  PDB: A:90-155 UniProt: 90-155                       ------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:78-117 UniProt: 1-117  --------------------------------Exon 1.3c          Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2  PDB: A:117-150          ----------------- Transcript 1 (2)
                 2i3i A  78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPGCQFLLRSKGQEYINNIH 167
                                    87        97       107       117       127       137       147       157       167

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with BIRC7_HUMAN | Q96CA5 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:95
                                    87        97       107       117       127       137       147       157       167     
          BIRC7_HUMAN    78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPSCQFLLRSKGRDFVHSVQETHSQ 172
               SCOP domains d2i3ib_ B: BIR-containing protein 7 (ML-IAP, livin)                                             SCOP domains
               CATH domains 2i3iB00 B:78-172 Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------BIR_REPEAT_1  PDB: B:87-154 UniProt: 87-154                         ------------------ PROSITE (1)
                PROSITE (2) ------------BIR_REPEAT_2  PDB: B:90-155 UniProt: 90-155                       ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: B:78-117 UniProt: 1-117  --------------------------------Exon 1.3c [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2  PDB: B:117-150          ---------------------- Transcript 1 (2)
                 2i3i B  78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPGCQFLLRSKGQEYINNIHLTHSL 172
                                    87        97       107       117       127       137       147       157       167

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	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(

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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( (-)

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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: BIR-containing protein 7 (ML-IAP, livin) (8)

Human (Homo sapiens) [TaxId: 9606] (8)

1a	d2i3ia_	A:
1b	d2i3ib_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A (42)

Homologous Superfamily: Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A (42)

Human (Homo sapiens) (35)

1a	2i3iB00	B:78-172
1b	2i3iA00	A:78-167

(no "Pfam Domain" information available for 2I3I)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BIRC7_HUMAN | Q96CA5)

molecular function
	GO:0004869	cysteine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	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:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0007257	activation of JUN kinase activity	The initiation of the activity of the inactive enzyme JUN kinase (JNK).
	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:1990001	inhibition of cysteine-type endopeptidase activity involved in apoptotic process	Any process that prevents the activation of an inactive cysteine-type endopeptidase involved in an apoptotic process.
	GO:0090307	mitotic spindle assembly	The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0070247	regulation of natural killer cell apoptotic process	Any process that modulates the occurrence or rate of natural killer cell death by apoptotic process.
	GO:0009966	regulation of signal transduction	Any process that modulates the frequency, rate or extent of signal transduction.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005876	spindle microtubule	Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.

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	BIRC7_HUMAN \| Q96CA5	:	1oxn 1oxq 1oy7 1tw6 2i3h 3f7g 3f7h 3f7i 3gt9 3gta 3uw5 4auq

1oxn	WILDTYPE ML-IAP-BIR BOUND TO AEAVPWKSE PEPTIDE
1oxq	WILDTYPE ML-IAP-BIR BOUND TO AVPIAQKSE (SMAC) PEPTIDE
1oy7	WILDTYPE ML-IAP-BIR BOUND TO AEVVAVKSE PEPTIDE
1tw6	ML-IAP/XIAP CHIMERA BOUND TO A 9MER PEPTIDE DERIVED FROM SMAC

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Ligands, Modified Residues, Ions (5, 8)

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