2R8X

Crystal structure of YrbI phosphatase from Escherichia coli

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	d2r8xa_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2r8xb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2r8xc_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2r8xd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2r8xe_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2r8xf_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2r8xg_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d2r8xh_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d2r8xi_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d2r8xj_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d2r8xk_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d2r8xl_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
M	d2r8xm_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
N	d2r8xn_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
O	d2r8xo_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
P	d2r8xp_	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)
A	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	HAD-like	8081274	3001890	SCOP2B (2022-06-29)
P	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)
A	Hydrolase_3	e2r8xA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
B	Hydrolase_3	e2r8xB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
C	Hydrolase_3	e2r8xC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
D	Hydrolase_3	e2r8xD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
E	Hydrolase_3	e2r8xE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
F	Hydrolase_3	e2r8xF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
G	Hydrolase_3	e2r8xG1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
H	Hydrolase_3	e2r8xH1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
I	Hydrolase_3	e2r8xI1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
J	Hydrolase_3	e2r8xJ1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
K	Hydrolase_3	e2r8xK1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
L	Hydrolase_3	e2r8xL1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
M	Hydrolase_3	e2r8xM1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
N	Hydrolase_3	e2r8xN1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
O	Hydrolase_3	e2r8xO1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
P	Hydrolase_3	e2r8xP1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
C	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)
E	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)
G	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)
I	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)
K	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)
M	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)
O	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
P	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 cation binding ion binding binding metal ion binding small molecule binding	lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process cellular biosynthetic process carbohydrate biosynthetic process cellular metabolic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process organic substance metabolic process lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process cellular biosynthetic process carbohydrate biosynthetic process cellular metabolic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process organic substance metabolic process biosynthetic process organic substance 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	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 National Science Foundation (DBI-1832184), 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.