3F7H - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

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

Date :   09 Nov 08 (Deposition) - 17 Mar 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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, Apoptosis, Metal-Binding, Nucleus, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Cohen, B. Alicke, L. O. Elliott, J. A. Flygare, T. Goncharov, S. F. Keteltas, M. C. Franklin, S. Frankovitz, J. P. Stephan, V. Tsui, D. Vucic, H. Wong, W. J. Fairbrother
Orally Bioavailable Antagonists Of Inhibitor Of Apoptosis Proteins Based On An Azabicyclooctane Scaffold
J. Med. Chem. V. 52 1723 2009
PubMed-ID: 19228017 | Reference-DOI: 10.1021/JM801450C
(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
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ML-IAP RESIDUES 63-172
	Gene	:	BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344
	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, RING FINGER PROTEIN 50

		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	419	2	Ligand/Ion	N-[(3AR,6S,6AS)-1-(N-METHYL-L-ALANYL-3-METHYL-L-VALYL)OCTAHYDROCYCLOPENTA[B]PYRROL-6-YL]-2,2-DIPHENYLACETAMIDE
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	419	1	Ligand/Ion	N-[(3AR,6S,6AS)-1-(N-METHYL-L-ALANYL-3-METHYL-L-VALYL)OCTAHYDROCYCLOPENTA[B]PYRROL-6-YL]-2,2-DIPHENYLACETAMIDE
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	419	1	Ligand/Ion	N-[(3AR,6S,6AS)-1-(N-METHYL-L-ALANYL-3-METHYL-L-VALYL)OCTAHYDROCYCLOPENTA[B]PYRROL-6-YL]-2,2-DIPHENYLACETAMIDE
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	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 , HOH A:287 , ARG B:136	BINDING SITE FOR RESIDUE 419 A 1
3	AC3	SOFTWARE	CYS B:124 , CYS B:127 , HIS B:144 , CYS B:151	BINDING SITE FOR RESIDUE ZN B 1001
4	AC4	SOFTWARE	SER B:93 , ASP B:96 , HIS B:115 , EDO B:174	BINDING SITE FOR RESIDUE LI B 1002
5	AC5	SOFTWARE	PRO A:104 , GLU A:106 , LEU A:107 , ASP A:139 , LYS B:121 , VAL B:122 , 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:288 , HOH B:305	BINDING SITE FOR RESIDUE 419 B 1
6	AC6	SOFTWARE	PRO B:82 , LYS B:146 , TRP B:147 , HIS B:167 , HIS B:170 , HOH B:192 , HOH B:276 , HOH B:300	BINDING SITE FOR RESIDUE BTB B 173
7	AC7	SOFTWARE	SER A:93 , HOH B:31 , SER B:93 , ASP B:96 , HIS B:115 , GLY B:117 , HOH B:236 , HOH B:265 , LI B:1002	BINDING SITE FOR RESIDUE EDO B 174
8	AC8	SOFTWARE	CYS B:127 , PHE B:148 , PRO B:149 , GLY B:150 , HOH B:204 , HOH B:240	BINDING SITE FOR RESIDUE EDO B 175

(no "SS Bond" information available for 3F7H)

(no "Cis Peptide Bond" information available for 3F7H)

(no "SAP(SNP)/Variant" information available for 3F7H)

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

(no "Exon" information available for 3F7H)

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: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 d3f7ha_ A: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------ Transcript
                 3f7h A  78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPGCQFLLRSKGQEYINNIH 167
                                    87        97       107       117       127       137       147       157       167

Chain A from PDB  Type:PROTEIN  Length:90
 aligned with Q6R308_HUMAN | Q6R308 from UniProtKB/TrEMBL  Length:224

    Alignment length:90
                                    87        97       107       117       127       137       147       157       167
         Q6R308_HUMAN    78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPSCQFLLRSKGRDFVHSVQ 167
               SCOP domains d3f7ha_ A: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..........hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3f7h A  78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPGCQFLLRSKGQEYINNIH 167
                                    87        97       107       117       127       137       147       157       167

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with BIRC7_HUMAN | Q96CA5 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:93
                                    87        97       107       117       127       137       147       157       167   
          BIRC7_HUMAN    78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPSCQFLLRSKGRDFVHSVQETH 170
               SCOP domains d3f7hb_ B: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh 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 --------------------------------------------------------------------------------------------- Transcript
                 3f7h B  78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPGCQFLLRSKGQEYINNIHLTH 170
                                    87        97       107       117       127       137       147       157       167

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with Q6R308_HUMAN | Q6R308 from UniProtKB/TrEMBL  Length:224

    Alignment length:93
                                    87        97       107       117       127       137       147       157       167   
         Q6R308_HUMAN    78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPSCQFLLRSKGRDFVHSVQETH 170
               SCOP domains d3f7hb_ B: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh......hhhhhhhh.eee......eee.....ee.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3f7h B  78 GPAFPGMGSEELRLASFYDWPLTAEVPPELLAAAGFFHTGHQDKVRCFFCYGGLQSWKRGDDPWTEHAKWFPGCQFLLRSKGQEYINNIHLTH 170
                                    87        97       107       117       127       137       147       157       167

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

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	d3f7ha_	A:
1b	d3f7hb_	B:

(no "CATH Domain" information available for 3F7H)

(no "Pfam Domain" information available for 3F7H)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q6R308_HUMAN | Q6R308)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3f7h)

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	3f7h
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Description

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Ligands, Modified Residues, Ions (5, 8)

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