5H7D | pdb_00005h7d

Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
N	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	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)
P	ECH_1	e5h7dP1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)
O	ECH_1	e5h7dO1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)
L	ECH_1	e5h7dL1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)
K	ECH_1	e5h7dK1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)
H	ECH_1	e5h7dH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)
G	ECH_1	e5h7dG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)
D [auth F]	ECH_1	e5h7dF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)
C [auth E]	ECH_1	e5h7dE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)
N	Brix	e5h7dN1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
M	Brix	e5h7dM1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
J	Brix	e5h7dJ1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
I	Brix	e5h7dI1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
F [auth D]	Brix	e5h7dD1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
E [auth C]	Brix	e5h7dC1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
B	Brix	e5h7dB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
A	Brix	e5h7dA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth E], D [auth F], G, H, K, C [auth E], D [auth F], G, H, K, L, O, P	PF13499	EF-hand domain pair (EF-hand_7)	EF-hand domain pair		Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	PF00202	Aminotransferase class-III (Aminotran_3)	Aminotransferase class-III		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F], G, H, K, C [auth E], D [auth F], G, H, K, L, O, P	Zpa963,Calmodulin	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding enzyme regulator activity molecular function regulator activity	establishment of organelle localization cellular localization sexual reproduction reproductive process microtubule cytoskeleton organization establishment of meiotic spindle localization spindle localization establishment or maintenance of cell polarity meiotic cell cycle process cellular component organization localization establishment of spindle localization establishment of spindle orientation organelle localization establishment of localization in cell establishment of organelle localization cellular localization sexual reproduction reproductive process microtubule cytoskeleton organization establishment of meiotic spindle localization spindle localization establishment or maintenance of cell polarity meiotic cell cycle process cellular component organization localization establishment of spindle localization establishment of spindle orientation organelle localization establishment of localization in cell cell cycle cellular component organization or biogenesis cell cycle process establishment of meiotic spindle orientation meiotic cell cycle establishment of localization establishment of cell polarity organelle organization cellular process microtubule-based process cytoskeleton organization regulation of localization regulation of biological process regulation of protein localization macromolecule localization biological regulation intracellular protein localization positive chemotaxis chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion regulation of cellular process regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death regulation of cell cycle regulation of biosynthetic process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching anatomical structure development embryo development import into cell transport phagocytosis apoptotic cell clearance endocytosis vesicle-mediated transport cell migration cell motility	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane phosphatase complex membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane phosphatase complex protein-containing complex catalytic complex calcineurin complex protein serine/threonine phosphatase complex intracellular protein-containing complex centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cell periphery cytoplasm mitotic spindle spindle
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	Putrescine aminotransferase,Immunoglobulin G-binding protein A	protein-containing complex binding binding immunoglobulin binding IgG binding transferase activity, transferring nitrogenous groups diamine:2-oxoglutarate transaminase activity transaminase activity transferase activity catalytic activity putrescine:2-oxoglutarate transaminase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding binding immunoglobulin binding IgG binding transferase activity, transferring nitrogenous groups diamine:2-oxoglutarate transaminase activity transaminase activity transferase activity catalytic activity putrescine:2-oxoglutarate transaminase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding	catabolic process oxoacid metabolic process L-lysine catabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process catabolic process oxoacid metabolic process L-lysine catabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process polyamine metabolic process biogenic amine catabolic process amine metabolic process putrescine catabolic process putrescine metabolic process polyamine catabolic process biogenic amine metabolic process amine catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E], D [auth F], G, H, K, C [auth E], D [auth F], G, H, K, L, O, P	IPR050230	Calmodulin/Myosin light chain/Troponin C-like	Family
C [auth E], D [auth F], G, H, K, C [auth E], D [auth F], G, H, K, L, O, P	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
C [auth E], D [auth F], G, H, K, C [auth E], D [auth F], G, H, K, L, O, P	IPR002048	EF-hand domain	Domain
C [auth E], D [auth F], G, H, K, C [auth E], D [auth F], G, H, K, L, O, P	IPR011992	EF-hand domain pair	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR005877	YSIRK Gram-positive signal peptide	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR036779	LysM domain superfamily	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR005038	Octapeptide repeat	Repeat
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR003132	Protein A, Ig-binding domain	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR018392	LysM domain	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR019931	LPXTG cell wall anchor motif	Conserved Site
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR049704	Aminotransferases class-III pyridoxal-phosphate attachment site	Conserved Site
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR050103	Class-III Pyridoxal-phosphate-dependent Aminotransferase	Family
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR017747	Putrescine aminotransferase	Family
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, M, N	IPR005814	Aminotransferase class-III	Family

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.