5W5Z

Crystal structure of BAXP168G in complex with an activating antibody at high resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth L]	d5w5zl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth H]	d5w5zh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth L]	PF07654	e5w5zL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A [auth L]	PF07686	e5w5zL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth H]	PF07654	e5w5zH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth H]	PF07686	e5w5zH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth A]	PF00452	e5w5zA1	A: alpha arrays	X: Toxins' membrane translocation domains	H: Bcl-2 inhibitors of programmed cell death (From Topology)	T: Bcl-2 inhibitors of programmed cell death	F: PF00452	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth L]	Fab 3C10	L-KAPPA	Rattus norvegicus (Norway rat)	IGKV22S401, IGKV22S701, IGKJ501, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	(VH-CH1)_L-KAPPA	IMGT (202417-0)
B [auth H]	Fab 3C10	VH-CH1	Rattus norvegicus (Norway rat)	IGHV1-2801, IGHJ201, IGHG2A*01	V-DOMAIN VH, C-DOMAIN CH1	IG	(VH-CH1)_L-KAPPA	IMGT (202417-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV22	Kappa	apoptosis regulator bax	SAbDab (2024-05-03)
B [auth H]	Heavy Chain	IGHV1	-	apoptosis regulator bax	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	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
A [auth L]	3C10 Fab light chain	-	-	-
B [auth H]	3C10 Fab heavy chain	-	-	-
C [auth A]	Apoptosis regulator BAX	death domain binding protein binding binding BH3 domain binding BH domain binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity lipid binding protein heterodimerization activity Hsp70 protein binding protein-folding chaperone binding heat shock protein binding death domain binding protein binding binding BH3 domain binding BH domain binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity lipid binding protein heterodimerization activity Hsp70 protein binding protein-folding chaperone binding heat shock protein binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity	inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis endoplasmic reticulum calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of protein binding regulation of molecular function inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis endoplasmic reticulum calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of protein binding regulation of molecular function negative regulation of protein binding negative regulation of binding regulation of binding biological regulation negative regulation of molecular function organelle fusion cellular component organization organelle organization cellular process mitochondrial fusion cellular component organization or biogenesis mitochondrion organization cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling signal transduction by p53 class mediator cell death intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death developmental process Sertoli cell proliferation multicellular organismal process cell population proliferation 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 epithelial cell proliferation system development development of secondary sexual characteristics B cell homeostasis multicellular organismal-level homeostasis leukocyte homeostasis immune system process homeostasis of number of cells lymphocyte homeostasis protein localization cellular localization establishment of protein localization establishment of protein localization to mitochondrial membrane protein insertion into mitochondrial membrane mitochondrial membrane organization localization cellular macromolecule localization establishment of localization in cell protein insertion into membrane membrane organization establishment of protein localization to membrane localization within membrane protein localization to membrane establishment of localization establishment of protein localization to organelle protein localization to organelle macromolecule localization protein localization to mitochondrion establishment of protein localization to mitochondrion response to chemical response to toxic substance regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity positive regulation of biological process positive regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process regulation of cysteine-type endopeptidase activity involved in apoptotic process organic substance metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process protein metabolic process activation of cysteine-type endopeptidase activity involved in apoptotic process activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process positive regulation of hydrolase activity positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis metabolic process macromolecule metabolic process regulation of metabolic process cellular developmental process cell development programmed cell death involved in cell development cell differentiation ectopic germ cell programmed cell death regulation of localization regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport regulation of calcium ion transport into cytosol transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport monoatomic cation transmembrane transport regulation of calcium ion transmembrane transport positive regulation of monoatomic ion transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport regulation of biological quality monoatomic cation transport regulation of metal ion transport positive regulation of cellular process calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport positive regulation of cytosolic calcium ion concentration inorganic ion transmembrane transport inorganic cation transmembrane transport transmembrane transport positive regulation of calcium ion transport into cytosol regulation of transmembrane transport positive regulation of transport regulation of cellular localization regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport calcium ion transport into cytosol response to organic substance cellular response to topologically incorrect protein cellular response to unfolded protein response to unfolded protein cellular response to chemical stimulus cellular response to stress response to stress response to topologically incorrect protein cellular response to organic substance apoptotic process involved in morphogenesis mammary gland morphogenesis apoptotic process involved in mammary gland involution mammary gland development gland development apoptotic process involved in development anatomical structure morphogenesis gland morphogenesis tissue remodeling mammary gland involution animal organ morphogenesis response to osmotic stress response to abiotic stimulus response to salt stress limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development apoptotic process involved in embryonic digit morphogenesis appendage morphogenesis embryonic digit morphogenesis limb morphogenesis apoptotic mitochondrial changes establishment or maintenance of transmembrane electrochemical gradient sexual reproduction multicellular organismal reproductive process cellular process involved in reproduction in multicellular organism gamete generation germ cell development neuron apoptotic process motor neuron apoptotic process pigmentation positive regulation of developmental pigmentation developmental pigmentation regulation of developmental pigmentation regulation of pigmentation regulation of mitochondrial membrane potential regulation of membrane potential lymphocyte apoptotic process leukocyte apoptotic process B cell apoptotic process epithelium development tissue development regulation of mammary gland epithelial cell proliferation mammary gland epithelium development regulation of cell population proliferation regulation of epithelial cell proliferation mammary gland epithelial cell proliferation head development hypothalamus development forebrain development brain development diencephalon development nervous system development central nervous system development limbic system development negative regulation of endoplasmic reticulum calcium ion concentration regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process negative regulation of phosphate metabolic process regulation of peptidyl-serine phosphorylation negative regulation of cellular metabolic process peptidyl-serine modification peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process peptidyl-amino acid modification protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of peptidyl-serine phosphorylation protein phosphorylation phosphorylation cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation mitochondrial fragmentation involved in apoptotic process immune response-regulating cell surface receptor signaling pathway extrinsic apoptotic signaling pathway positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway B cell receptor apoptotic signaling pathway activation of immune response negative regulation of signaling regulation of signal transduction regulation of programmed cell death negative regulation of cell communication negative regulation of apoptotic signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process negative regulation of signal transduction negative regulation of apoptotic process regulation of cell communication regulation of apoptotic signaling pathway catabolic process macromolecule catabolic process regulation of DNA catabolic process nucleobase-containing compound metabolic process execution phase of apoptosis positive regulation of DNA catabolic process DNA catabolic process apoptotic nuclear changes regulation of nucleobase-containing compound metabolic process regulation of apoptotic DNA fragmentation cellular component disassembly positive regulation of nucleobase-containing compound metabolic process positive regulation of apoptotic DNA fragmentation DNA metabolic process regulation of catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process positive regulation of catabolic process organic cyclic compound metabolic process apoptotic DNA fragmentation positive regulation of DNA metabolic process cellular component disassembly involved in execution phase of apoptosis nucleic acid catabolic process organic substance catabolic process regulation of DNA metabolic process myeloid cell homeostasis programmed necrotic cell death regulation of membrane permeability regulation of mitochondrial membrane permeability regulation of mitochondrial membrane permeability involved in programmed necrotic cell death mitochondrial transport negative regulation of sequestering of calcium ion maintenance of location in cell regulation of sequestering of calcium ion sequestering of calcium ion maintenance of location release of sequestered calcium ion into cytosol response to ionizing radiation response to radiation response to gamma radiation regulation of release of sequestered calcium ion into cytosol positive regulation of release of sequestered calcium ion into cytosol blood vessel morphogenesis tube development vasculature development circulatory system development tube morphogenesis apoptotic process involved in blood vessel morphogenesis blood vessel development regulation of developmental process positive regulation of apoptotic process involved in mammary gland involution positive regulation of developmental process positive regulation of apoptotic process involved in morphogenesis positive regulation of programmed cell death positive regulation of apoptotic process involved in development regulation of apoptotic process involved in development positive regulation of apoptotic process regulation of apoptotic process involved in morphogenesis camera-type eye morphogenesis sensory organ development eye development post-embryonic camera-type eye development visual system development post-embryonic camera-type eye morphogenesis eye morphogenesis post-embryonic eye morphogenesis sensory organ morphogenesis camera-type eye development post-embryonic development sensory system development response to wounding response to axon injury B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation B cell homeostatic proliferation leukocyte activation mononuclear cell proliferation lymphocyte proliferation positive regulation of epithelial cell apoptotic process regulation of epithelial cell apoptotic process epithelial cell apoptotic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis negative regulation of membrane potential negative regulation of mitochondrial membrane potential regulation of reproductive process positive regulation of reproductive process fertilization positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of release of cytochrome c from mitochondria positive regulation of release of cytochrome c from mitochondria regulation of organelle organization release of cytochrome c from mitochondria regulation of mitochondrion organization retina development in camera-type eye protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly positive regulation of neuron apoptotic process regulation of neuron apoptotic process extrinsic apoptotic signaling pathway via death domain receptors signal transduction in absence of ligand extrinsic apoptotic signaling pathway in absence of ligand positive regulation of IRE1-mediated unfolded protein response positive regulation of cell communication positive regulation of signal transduction regulation of cellular response to stress endoplasmic reticulum unfolded protein response regulation of response to endoplasmic reticulum stress regulation of endoplasmic reticulum unfolded protein response positive regulation of response to endoplasmic reticulum stress regulation of response to stress positive regulation of endoplasmic reticulum unfolded protein response response to endoplasmic reticulum stress regulation of IRE1-mediated unfolded protein response IRE1-mediated unfolded protein response positive regulation of signaling pallium development cerebral cortex development telencephalon development female gonad development female sex differentiation development of primary female sexual characteristics ovarian follicle development negative regulation of cell population proliferation fibroblast proliferation regulation of fibroblast proliferation negative regulation of fibroblast proliferation regulation of intrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway regulation of intracellular signal transduction positive regulation of intracellular signal transduction positive regulation of intrinsic apoptotic signaling pathway hemopoiesis B cell negative selection mononuclear cell differentiation lymphocyte differentiation B cell differentiation B cell selection leukocyte differentiation release of matrix enzymes from mitochondria supramolecular fiber organization thymocyte apoptotic process T cell apoptotic process kidney development renal system development regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process regulation of B cell apoptotic process positive regulation of lymphocyte apoptotic process positive regulation of B cell apoptotic process positive regulation of leukocyte apoptotic process membrane lipid metabolic process glycosphingolipid metabolic process glycolipid metabolic process liposaccharide metabolic process carbohydrate derivative metabolic process sphingolipid metabolic process cellular lipid metabolic process lipid metabolic process genitalia development female genitalia development vagina development positive regulation of motor neuron apoptotic process regulation of motor neuron apoptotic process odontogenesis of dentin-containing tooth odontogenesis negative regulation of neuron apoptotic process DNA damage response intrinsic apoptotic signaling pathway in response to DNA damage blood vessel remodeling T cell homeostatic proliferation T cell homeostasis T cell activation T cell proliferation response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus cellular response to abiotic stimulus cellular response to UV response to nutrient levels regulation of response to nutrient levels nitrogen utilization regulation of nitrogen utilization intracellular nitrogen homeostasis intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress neuron migration generation of neurons neurogenesis cell migration cell motility cell cycle regulation of cell cycle retinal cell programmed cell death spermatid differentiation spermatogenesis male gamete generation mitochondrial outer membrane permeabilization involved in programmed cell death positive regulation of mitochondrial membrane permeability involved in apoptotic process positive regulation of mitochondrial membrane permeability positive regulation of membrane permeability regulation of mitochondrial membrane permeability involved in apoptotic process cellular response to virus biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	protein-containing complex BAX complex Bcl-2 family protein complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cytoplasm protein-containing complex BAX complex Bcl-2 family protein complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol membrane pore complex membrane protein complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane mitochondrial permeability transition pore complex mitochondrial protein-containing complex mitochondrion mitochondrial envelope extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle mitochondrial membrane organelle outer membrane bounding membrane of organelle mitochondrial outer membrane outer membrane BAK complex

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: Q07812	polycystic ovary syndrome Alzheimer disease Myocardial Reperfusion Injury esophageal cancer primary cutaneous T-cell non-Hodgkin lymphoma intestinal cancer prostate cancer breast carcinoma malignant colon neoplasm myocardial infarction HIV infectious disease male infertility colorectal cancer medulloblastoma osteosarcoma polycystic ovary syndrome Alzheimer disease Myocardial Reperfusion Injury esophageal cancer primary cutaneous T-cell non-Hodgkin lymphoma intestinal cancer prostate cancer breast carcinoma malignant colon neoplasm myocardial infarction HIV infectious disease male infertility colorectal cancer medulloblastoma osteosarcoma glioblastoma psoriasis spina bifida intracerebral hemorrhage tuberculosis breast cancer lymphoma colonic neoplasm cutaneous lupus erythematosus neoplasm of esophagus peripheral nervous system disease granulomatous slack skin disease acute kidney failure acute T cell leukemia intestinal neoplasm large cell medulloblastoma colorectal adenocarcinoma drug-induced liver injury gastric carcinoma peripheral neuropathy adrenal cortex carcinoma ischemic disease benign colon neoplasm leukemia, acute lymphocytic, susceptibility to, 1 Burkitt lymphoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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 R01GM133198.