2R8Y | pdb_00002r8y

Crystal structure of YrbI phosphatase from Escherichia coli in a complex with Ca

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	d2r8yp_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
O	d2r8yo_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
N	d2r8yn_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
M	d2r8ym_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d2r8yl_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d2r8yk_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d2r8yj_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d2r8yi_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d2r8yh_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2r8yg_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2r8yf_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2r8ye_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2r8yd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2r8yc_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2r8yb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2r8ya_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	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	e2r8yP1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
O	HRM	e2r8yO1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
N	HRM	e2r8yN1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
M	HRM	e2r8yM1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
L	HRM	e2r8yL1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
K	HRM	e2r8yK1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
J	HRM	e2r8yJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
I	HRM	e2r8yI1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
H	HRM	e2r8yH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
G	HRM	e2r8yG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
F	HRM	e2r8yF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
E	HRM	e2r8yE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
D	HRM	e2r8yD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
C	HRM	e2r8yC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
B	HRM	e2r8yB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HRM	ECOD (v294.1)
A	HRM	e2r8yA1	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	YrbI from Escherichia coli	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.