3UX7 | pdb_00003ux7

Crystal structure of a dimeric myotoxic component of the Vipera ammodytes meridionalis venom reveals determinants of myotoxicity and membrane damaging activity

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3ux7a_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	automated matches	(Vipera ammodytes meridionalis ) [TaxId: 73841 ],	SCOPe (2.08)
B	d3ux7b_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	automated matches	(Vipera ammodytes meridionalis ) [TaxId: 73841 ],	SCOPe (2.08)
C	d3ux7c_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	automated matches	(Vipera ammodytes meridionalis ) [TaxId: 73841 ],	SCOPe (2.08)
D	d3ux7d_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	automated matches	(Vipera ammodytes meridionalis ) [TaxId: 73841 ],	SCOPe (2.08)
E	d3ux7e_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	automated matches	(Vipera ammodytes meridionalis ) [TaxId: 73841 ],	SCOPe (2.08)
F	d3ux7f_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	automated matches	(Vipera ammodytes meridionalis ) [TaxId: 73841 ],	SCOPe (2.08)
G	d3ux7g_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	automated matches	(Vipera ammodytes meridionalis ) [TaxId: 73841 ],	SCOPe (2.08)
H	d3ux7h_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	automated matches	(Vipera ammodytes meridionalis ) [TaxId: 73841 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Vertebrate phospholipase A2	8062736	4001493	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phospholipase A2, PLA2	8062737	3001690	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Phospholipase A2, PLA2	8062737	3001690	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phospholipase A2, PLA2	8062737	3001690	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phospholipase A2, PLA2	8062737	3001690	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phospholipase A2, PLA2	8062737	3001690	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phospholipase A2, PLA2	8062737	3001690	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phospholipase A2, PLA2	8062737	3001690	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Phospholipase A2, PLA2	8062737	3001690	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	Phospholip_A2_1	e3ux7A1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)
B	Phospholip_A2_1	e3ux7B1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)
C	Phospholip_A2_1	e3ux7C1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)
D	Phospholip_A2_1	e3ux7D1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)
E	Phospholip_A2_1	e3ux7E1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)
F	Phospholip_A2_1	e3ux7F1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)
G	Phospholip_A2_1	e3ux7G1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)
H	Phospholip_A2_1	e3ux7H1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.3.0)
B	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.3.0)
C	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.3.0)
D	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.3.0)
E	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.3.0)
F	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.3.0)
G	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.3.0)
H	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00068	Phospholipase A2 (Phospholip_A2_1)	Phospholipase A2	Phospholipase A2 releases fatty acids from the second carbon group of glycerol. Perhaps the best known members are secreted snake venoms, but also found in secreted pancreatic and membrane-associated forms. Structure is all-alpha, with two core disul ...	Phospholipase A2 releases fatty acids from the second carbon group of glycerol. Perhaps the best known members are secreted snake venoms, but also found in secreted pancreatic and membrane-associated forms. Structure is all-alpha, with two core disulfide-linked helices and a calcium-binding loop. This alignment represents the major family of PLA2s. A second minor family, defined by the honeybee venom PLA2 PDB:1POC and related sequences from Gila monsters (Heloderma), is not recognised. This minor family conserves the core helix pair but is substantially different elsewhere. The PROSITE pattern PA2_HIS, specific to the first core helix, recognises both families.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Ammodytin L(1) isoform	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding phospholipase A2 activity calcium-dependent phospholipase A2 activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity hydrolase activity catalytic activity phospholipase activity lipase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding phospholipase A2 activity calcium-dependent phospholipase A2 activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity hydrolase activity catalytic activity phospholipase activity lipase activity phospholipid binding lipid binding	organic anion transport carboxylic acid transport secretion transport arachidonate transport lipid localization lipid transport establishment of localization organic acid transport localization arachidonate secretion monocarboxylic acid transport fatty acid transport icosanoid transport macromolecule localization organic anion transport carboxylic acid transport secretion transport arachidonate transport lipid localization lipid transport establishment of localization organic acid transport localization arachidonate secretion monocarboxylic acid transport fatty acid transport icosanoid transport macromolecule localization icosanoid secretion long-chain fatty acid transport lipid catabolic process catabolic process metabolic process cellular process primary metabolic process lipid metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation regulation of biological process cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion biological regulation cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR033112	Phospholipase A2, aspartic acid active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR033113	Phospholipase A2, histidine active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001211	Phospholipase A2	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036444	Phospholipase A2 domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR016090	Phospholipase A2 domain	Domain

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.