3CM2

Crystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth D]	d3cm2d_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d3cm2a_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth C]	d3cm2c_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3cm2e_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3cm2f_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3cm2g_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d3cm2i_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d3cm2j_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d3cm2b_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d3cm2h_	Small proteins	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	Inhibitor of apoptosis (IAP) repeat	BIR domains of XIAP	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Inhibitor of apoptosis (IAP) repeat	8037741	3001510	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth D]	BIR	e3cm2D1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
B [auth A]	BIR	e3cm2A1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
D [auth C]	BIR	e3cm2C1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
E	BIR	e3cm2E1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
F	BIR	e3cm2F1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
G	BIR	e3cm2G1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
I	BIR	e3cm2I1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
J	BIR	e3cm2J1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
C [auth B]	BIR	e3cm2B1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)
H	BIR	e3cm2H1	A: few secondary structure elements	X: Inhibitor of apoptosis (IAP) repeat (From Topology)	H: Inhibitor of apoptosis (IAP) repeat (From Topology)	T: Inhibitor of apoptosis (IAP) repeat	F: BIR	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth D]	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
B [auth A]	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
D [auth C]	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
E	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
F	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
G	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
I	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
J	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
C [auth B]	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)
H	1.10.1170.10	Mainly Alpha	Orthogonal Bundle	Inhibitor Of Apoptosis Protein (2mihbC-IAP-1)	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J	PF00653	Inhibitor of Apoptosis domain (BIR)	Inhibitor of Apoptosis domain	BIR stands for 'Baculovirus Inhibitor of apoptosis protein Repeat'. It is found repeated in inhibitor of apoptosis proteins (IAPs), and in fact it is also known as IAP repeat. These domains characteristically have a number of invariant residues, incl ...	BIR stands for 'Baculovirus Inhibitor of apoptosis protein Repeat'. It is found repeated in inhibitor of apoptosis proteins (IAPs), and in fact it is also known as IAP repeat. These domains characteristically have a number of invariant residues, including 3 conserved cysteines and one conserved histidine that coordinate a zinc ion. They are usually made up of 4-5 alpha helices and a three-stranded beta-sheet. BIR is also found in other proteins known as BIR-domain-containing proteins (BIRPs), such as Survivin (Swiss:O15392) [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J	Baculoviral IAP repeat-containing protein 4	enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity cysteine-type endopeptidase inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity cysteine-type endopeptidase inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cysteine-type endopeptidase inhibitor activity involved in apoptotic process cysteine-type endopeptidase regulator activity involved in apoptotic process protein binding binding protein serine/threonine kinase binding kinase binding enzyme binding protein kinase binding cation binding ion binding metal ion binding small molecule binding identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway response to biotic stimulus immune response-activating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process innate immune response-activating signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress innate immune response response to external biotic stimulus nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway positive regulation of innate immune response defense response regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway defense response to symbiont immune system process negative regulation of hydrolase activity negative regulation of proteolysis regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of programmed cell death negative regulation of endopeptidase activity regulation of primary metabolic process negative regulation of peptidase activity regulation of cysteine-type endopeptidase activity involved in apoptotic process organic substance metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity negative regulation of cellular process negative regulation of cysteine-type endopeptidase activity involved in apoptotic process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process negative regulation of programmed cell death regulation of protein metabolic process regulation of apoptotic process negative regulation of metabolic process regulation of peptidase activity negative regulation of molecular function primary metabolic process regulation of macromolecule metabolic process cell death regulation of molecular function negative regulation of apoptotic process regulation of hydrolase activity negative regulation of cysteine-type endopeptidase activity metabolic process macromolecule metabolic process apoptotic process regulation of metabolic process programmed cell death nucleotide-binding oligomerization domain containing 1 signaling pathway regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal defense response to bacterium response to bacterium regulation of protein maturation negative regulation of cellular metabolic process protein maturation organic substance biosynthetic process zymogen inhibition cellular metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of protein processing protein processing regulation of macromolecule biosynthetic process negative regulation of protein maturation cellular biosynthetic process inhibition of cysteine-type endopeptidase activity regulation of biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of protein processing inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis copper ion homeostasis monoatomic cation homeostasis nucleotide-binding oligomerization domain containing 2 signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cellular response to endogenous stimulus BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor positive regulation of JNK cascade JNK cascade positive regulation of MAPK cascade regulation of JNK cascade regulation of MAPK cascade MAPK cascade protein polyubiquitination protein K63-linked ubiquitination regulation of inflammatory response inflammatory response neuron apoptotic process cell population proliferation regulation of cell population proliferation Wnt signaling pathway positive regulation of protein linear polyubiquitination regulation of protein linear polyubiquitination regulation of protein polyubiquitination positive regulation of protein polyubiquitination protein linear polyubiquitination regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of Wnt signaling pathway regulation of apoptosis involved in tissue homeostasis multicellular organismal process homeostasis of number of cells within a tissue tissue homeostasis multicellular organismal-level homeostasis anatomical structure homeostasis homeostasis of number of cells cell cycle regulation of cell cycle positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of type I interferon production type I interferon production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of cellular biosynthetic process regulation of type I interferon production response to organic substance negative regulation of signaling response to cytokine negative regulation of cell communication cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus cellular response to organic substance regulation of tumor necrosis factor-mediated signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway negative regulation of tumor necrosis factor-mediated signaling pathway negative regulation of signal transduction regulation of response to cytokine stimulus cellular response to chemical stimulus negative regulation of response to cytokine stimulus negative regulation of cytokine-mediated signaling pathway response to chemical response to tumor necrosis factor	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J	IPR048875	BIRC2/3-like, UBA domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J	IPR011029	Death-like domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J	IPR042579	XIAP/BIRC8, UBA domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J	IPR001370	BIR repeat	Repeat
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H, I, J	Pharos: P98170	X-linked lymphoproliferative disease due to XIAP deficiency esophageal cancer ovarian cancer Mammary Neoplasms, Experimental amyotrophic lateral sclerosis type 1 osteosarcoma pancreatic ductal adenocarcinoma X-linked lymphoproliferative disease due to SH2D1A deficiency amyotrophic lateral sclerosis intellectual disability lymphatic system disease myopathy pancreatic intraductal papillary-mucinous carcinoma breast cancer facioscapulohumeral muscular dystrophy X-linked lymphoproliferative disease due to XIAP deficiency esophageal cancer ovarian cancer Mammary Neoplasms, Experimental amyotrophic lateral sclerosis type 1 osteosarcoma pancreatic ductal adenocarcinoma X-linked lymphoproliferative disease due to SH2D1A deficiency amyotrophic lateral sclerosis intellectual disability lymphatic system disease myopathy pancreatic intraductal papillary-mucinous carcinoma breast cancer facioscapulohumeral muscular dystrophy juvenile dermatomyositis neoplasm of esophagus ovarian neoplasm pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia X-linked lymphoproliferative syndrome cancer hematologic disease large cell medulloblastoma lymphoproliferative syndrome

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.