1RLM | pdb_00001rlm

Crystal Structure of ybiV from Escherichia coli K12

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)
D	d1rlmd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Predicted hydrolases Cof	Sugar phosphatase SupH (YbiV)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1rlmc_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Predicted hydrolases Cof	Sugar phosphatase SupH (YbiV)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1rlmb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Predicted hydrolases Cof	Sugar phosphatase SupH (YbiV)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1rlma_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Predicted hydrolases Cof	Sugar phosphatase SupH (YbiV)	(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)
D	SCOP2B Superfamily	HAD-like	8042274	3001890	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HAD-like	8042274	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8042274	3001890	SCOP2B (2022-06-29)
A	SCOP2 Family	Predicted hydrolases Cof	8029895	4002994	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HAD-like	8042274	3001890	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	S6PP	e1rlmD1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: S6PP	ECOD (develop294)
C	S6PP	e1rlmC1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: S6PP	ECOD (develop294)
B	S6PP	e1rlmB2	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: S6PP	ECOD (develop294)
A	Hydrolase_3	e1rlmA3	A: alpha bundles	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
D	3.30.1240.10	Alpha Beta	2-Layer Sandwich	Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase	Chain: A	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)
C	3.30.1240.10	Alpha Beta	2-Layer Sandwich	Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase	Chain: A	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)
B	3.30.1240.10	Alpha Beta	2-Layer Sandwich	Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase	Chain: A	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)
A	3.30.1240.10	Alpha Beta	2-Layer Sandwich	Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	Phosphatase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds carbohydrate phosphatase activity phosphatase activity hydrolase activity catalytic activity sugar-phosphatase activity fructose-1-phosphatase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds carbohydrate phosphatase activity phosphatase activity hydrolase activity catalytic activity sugar-phosphatase activity fructose-1-phosphatase activity sorbitol-6-phosphatase activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000150	Cof family	Family
A, B, C, D	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D	IPR006379	HAD-superfamily hydrolase, subfamily IIB	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.