2R8Z | pdb_00002r8z

Crystal structure of YrbI phosphatase from Escherichia coli in complex with a phosphate and a calcium ion

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)
P	d2r8zp_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
O	d2r8zo_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
N	d2r8zn_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
M	d2r8zm_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
L	d2r8zl_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
K	d2r8zk_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
J	d2r8zj_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
I	d2r8zi_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
H	d2r8zh_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
G	d2r8zg_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
F	d2r8zf_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
E	d2r8ze_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
D	d2r8zd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
C	d2r8zc_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
B	d2r8zb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
A	d2r8za_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8081274	3001890	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	HRM	e2r8zP1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
O	HRM	e2r8zO1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
N	HRM	e2r8zN1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
M	HRM	e2r8zM1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
L	HRM	e2r8zL1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
K	HRM	e2r8zK1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
J	HRM	e2r8zJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
I	HRM	e2r8zI1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
H	HRM	e2r8zH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
G	HRM	e2r8zG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
F	HRM	e2r8zF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
E	HRM	e2r8zE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
D	HRM	e2r8zD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
C	HRM	e2r8zC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
B	HRM	e2r8zB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
A	HRM	e2r8zA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
O	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
N	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
M	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
L	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
K	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
J	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
I	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
H	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
G	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
F	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
E	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
D	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
C	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	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, I, J, K, L, M, N, O, P	PF08282	haloacid dehalogenase-like hydrolase (Hydrolase_3)	haloacid dehalogenase-like hydrolase	This family contains haloacid dehalogenase-like hydrolase enzymes.	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, I, J, K, L, M, N, O, P	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase	phosphoric ester hydrolase activity 3-deoxy-manno-octulosonate-8-phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity N-acylneuraminate cytidylyltransferase activity cytidylyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding ion binding binding phosphoric ester hydrolase activity 3-deoxy-manno-octulosonate-8-phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity N-acylneuraminate cytidylyltransferase activity cytidylyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding ion binding binding metal ion binding small molecule binding	lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process biosynthetic process metabolic process lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR050793	CMP-NeuNAc synthase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR010023	KdsC family	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.