4YK9 | pdb_00004yk9

Complex structure of BCL-XL and mutated BIM BH3 domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth F]	ThiF	e4yk9F1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: ThiF	ECOD (v294.1)
A	ThiF	e4yk9A1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: ThiF	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth F]	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (4.3.0)
A	1.10.437.10	Mainly Alpha	Orthogonal Bundle	Apoptosis Regulator Bcl-x	Blc2-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth F]	PF02180	Bcl-2 homology region 4 (BH4)	Bcl-2 homology region 4	-	Family
A, C [auth F]	PF00452	Apoptosis regulator proteins, Bcl-2 family (Bcl-2)	Apoptosis regulator proteins, Bcl-2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D [auth G]	BH3BIM	-	-	-
A, C [auth F]	Bcl-2-like protein 1	protein binding binding BH domain binding protein domain specific binding death domain binding BH3 domain binding protein-containing complex binding identical protein binding clathrin binding MDM2/MDM4 family protein binding enzyme binding GTPase binding enzyme regulator activity cysteine-type endopeptidase inhibitor activity involved in apoptotic process protein binding binding BH domain binding protein domain specific binding death domain binding BH3 domain binding protein-containing complex binding identical protein binding clathrin binding MDM2/MDM4 family protein binding enzyme binding GTPase binding enzyme regulator activity cysteine-type endopeptidase inhibitor activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process kinase binding protein kinase binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development spermatogenesis sexual reproduction multicellular organismal reproductive process male gamete generation gamete generation fertilization response to stimulus response to stress response to ischemia cellular response to stimulus extrinsic apoptotic signaling pathway via death domain receptors regulation of cellular process signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of cell communication cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process signal transduction regulation of biological process regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of extrinsic apoptotic signaling pathway via death domain receptors cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of cell communication cellular process apoptotic process programmed cell death regulation of apoptotic signaling pathway cell population proliferation regulation of growth growth positive regulation of programmed cell death positive regulation of biological process positive regulation of apoptotic process positive regulation of cellular process response to radiation response to abiotic stimulus regulation of anoikis negative regulation of anoikis anoikis cellular response to nitrogen compound cellular response to chemical stimulus response to chemical response to nitrogen compound cellular response to alkaloid response to alkaloid regulation of localization apoptotic mitochondrial changes localization regulation of biological quality positive regulation of membrane permeability negative regulation of cellular component organization establishment of localization regulation of organelle organization regulation of membrane permeability negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway regulation of mitochondrial membrane permeability involved in apoptotic process regulation of cellular component organization negative regulation of mitochondrial membrane permeability transport mitochondrial outer membrane permeabilization involved in programmed cell death cellular component organization positive regulation of mitochondrial membrane permeability involved in apoptotic process positive regulation of mitochondrial membrane permeability cellular component organization or biogenesis regulation of mitochondrial membrane permeability mitochondrion organization regulation of transport organelle organization negative regulation of organelle organization regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway regulation of mitochondrion organization negative regulation of membrane permeability mitochondrial outer membrane permeabilization import into cell cellular localization synaptic vesicle cycle regulation of synaptic vesicle recycling vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling regulation of synaptic vesicle endocytosis establishment of localization in cell regulation of endocytosis synaptic vesicle endocytosis regulation of vesicle-mediated transport endocytosis embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development apoptotic process in bone marrow cell signal transduction in absence of ligand extrinsic apoptotic signaling pathway in absence of ligand regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division cell cycle regulation of cell cycle cell cycle process female gonad development female sex differentiation development of primary female sexual characteristics ovarian follicle development regulation of release of cytochrome c from mitochondria negative regulation of release of cytochrome c from mitochondria release of cytochrome c from mitochondria cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid positive regulation of cell communication regulated exocytosis positive regulation of neurotransmitter secretion synaptic vesicle exocytosis positive regulation of regulated secretory pathway trans-synaptic signaling positive regulation of neurotransmitter transport neurotransmitter secretion regulation of synaptic vesicle exocytosis positive regulation of synaptic transmission neurotransmitter transport regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis modulation of chemical synaptic transmission positive regulation of secretion by cell positive regulation of exocytosis regulation of regulated secretory pathway synaptic signaling regulation of secretion by cell secretion by cell positive regulation of secretion signal release positive regulation of synaptic vesicle exocytosis secretion regulation of neurotransmitter transport export from cell cell-cell signaling chemical synaptic transmission positive regulation of transport regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis positive regulation of signaling response to ketone response to cycloheximide response to alcohol response to oxygen-containing compound nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process positive regulation of phosphate metabolic process purine ribonucleoside triphosphate biosynthetic process positive regulation of nucleotide biosynthetic process regulation of nucleotide biosynthetic process regulation of primary metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process ribonucleotide biosynthetic process purine nucleoside triphosphate biosynthetic process regulation of small molecule metabolic process positive regulation of purine nucleotide biosynthetic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process positive regulation of phosphorus metabolic process primary metabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process ribonucleoside triphosphate biosynthetic process positive regulation of ATP metabolic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process regulation of metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process positive regulation of nucleotide metabolic process purine nucleotide metabolic process ribonucleotide metabolic process positive regulation of biosynthetic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process purine-containing compound biosynthetic process purine nucleoside triphosphate metabolic process regulation of biosynthetic process carbohydrate derivative biosynthetic process regulation of purine nucleotide biosynthetic process nucleoside triphosphate biosynthetic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of ATP biosynthetic process regulation of ATP biosynthetic process organophosphate metabolic process positive regulation of small molecule metabolic process negative regulation of intracellular signal transduction regulation of cellular response to stress regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cellular response to stress regulation of intracellular signal transduction regulation of response to stress intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage negative regulation of intrinsic apoptotic signaling pathway DNA damage response biological process involved in interspecies interaction between organisms defense response to virus defense response response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus regulation of protein localization negative regulation of protein localization to plasma membrane intracellular protein localization regulation of protein localization to membrane negative regulation of protein localization protein localization to cell periphery protein localization to plasma membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane negative regulation of protein localization to membrane regulation of cellular localization macromolecule localization negative regulation of protein localization to cell periphery regulation of protein localization to plasma membrane cellular developmental process cell development cellular process involved in reproduction in multicellular organism cell differentiation germ cell development cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation cellular response to abiotic stimulus response to gamma radiation regulation of mitochondrial membrane potential regulation of membrane potential regulation of response to endoplasmic reticulum stress negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway response to endoplasmic reticulum stress negative regulation of response to endoplasmic reticulum stress vesicle localization synaptic vesicle clustering organelle localization positive regulation of synaptic vesicle clustering regulation of synaptic vesicle clustering synaptic vesicle localization response to peptide response to cytokine neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process intracellular transport endosomal transport synaptic vesicle endosomal processing synaptic vesicle recycling via endosome negative regulation of execution phase of apoptosis regulation of execution phase of apoptosis execution phase of apoptosis positive regulation of cell population proliferation regulation of cell population proliferation hepatocyte apoptotic process epithelial cell apoptotic process negative regulation of synaptic transmission regulation of synaptic plasticity long-term synaptic depression regulation of long-term synaptic depression positive regulation of cellular component organization positive regulation of synaptic vesicle recycling positive regulation of endocytosis positive regulation of synaptic vesicle endocytosis	cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle intracellular organelle organelle envelope organelle nuclear envelope organelle membrane cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle intracellular organelle organelle envelope organelle nuclear envelope organelle membrane mitochondrial membrane mitochondrion mitochondrial envelope cytoplasm cytosol organelle outer membrane bounding membrane of organelle mitochondrial outer membrane outer membrane synapse intracellular vesicle transport vesicle membrane presynapse cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane cell junction vesicle transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle exocytic vesicle organelle inner membrane mitochondrial inner membrane centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton protein-containing complex Bcl-2 family protein complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth F]	IPR036834	Bcl-2-like superfamily	Homologous Superfamily
A, C [auth F]	IPR004725	Apoptosis regulator, Bcl-2/ BclX	Family
A, C [auth F]	IPR003093	Apoptosis regulator, Bcl-2 protein, BH4	Domain
A, C [auth F]	IPR002475	Bcl2-like	Family
A, C [auth F]	IPR020731	Apoptosis regulator, Bcl-2, BH4 motif, conserved site	Conserved Site
A, C [auth F]	IPR013279	Apoptosis regulator, Bcl-X	Family
A, C [auth F]	IPR020728	Apoptosis regulator, Bcl-2, BH3 motif, conserved site	Conserved Site
A, C [auth F]	IPR020726	Apoptosis regulator, Bcl-2, BH2 motif, conserved site	Conserved Site
A, C [auth F]	IPR046371	Bcl-2, Bcl-2 homology region 1-3	Domain
A, C [auth F]	IPR026298	Bcl-2 family	Family
A, C [auth F]	IPR020717	Apoptosis regulator, Bcl-2, BH1 motif, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D [auth G]	AAR	Parent Component: ARG RESID: AA0082 PSI-MOD : L-arginine amide MOD:00091
B, D [auth G]	NLG	RESID: AA0082
B, D [auth G]	SEP	Parent Component: SER RESID: AA0082 , AA0037 PSI-MOD : L-arginine amide MOD:00091 , O-phospho-L-serine MOD:00046

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.