1RDF | pdb_00001rdf

G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate

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)
F	d1rdff_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Phosphonoacetaldehyde hydrolase-like	Phosphonoacetaldehyde hydrolase	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)
E	d1rdfe_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Phosphonoacetaldehyde hydrolase-like	Phosphonoacetaldehyde hydrolase	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)
D	d1rdfd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Phosphonoacetaldehyde hydrolase-like	Phosphonoacetaldehyde hydrolase	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)
C	d1rdfc_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Phosphonoacetaldehyde hydrolase-like	Phosphonoacetaldehyde hydrolase	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)
B	d1rdfb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Phosphonoacetaldehyde hydrolase-like	Phosphonoacetaldehyde hydrolase	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)
A	d1rdfa_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Phosphonoacetaldehyde hydrolase-like	Phosphonoacetaldehyde hydrolase	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	HAD-like	8042360	3001890	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HAD-like	8042360	3001890	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HAD-like	8042360	3001890	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HAD-like	8042360	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8042360	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8042360	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)
F	HAD_2	e1rdfF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
E	HAD_2	e1rdfE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
D	HAD_2	e1rdfD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
C	HAD_2	e1rdfC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
B	HAD_2	e1rdfB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
A	HAD_2	e1rdfA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
F	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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)
E	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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)
D	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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	PF00702	haloacid dehalogenase-like hydrolase (Hydrolase)	haloacid dehalogenase-like hydrolase	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted fo ...	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain [1]. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria [2].	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	phosphonoacetaldehyde hydrolase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphoglycolate phosphatase activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity phosphonoacetaldehyde hydrolase activity hydrolase activity, acting on acid carbon-phosphorus bonds	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair catabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair catabolic process organic phosphonate metabolic process oxoacid metabolic process organic phosphonate catabolic process small molecule metabolic process organic acid metabolic process phosphorus metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006439	HAD hydrolase, subfamily IA	Family
A, B, C, D, E A, B, C, D, E, F	IPR006323	Phosphonoacetaldehyde hydrolase	Family
A, B, C, D, E A, B, C, D, E, F	IPR050155	HAD-like hydrolase superfamily	Family
A, B, C, D, E A, B, C, D, E, F	IPR023198	Phosphoglycolate phosphatase-like, domain 2	Homologous Superfamily

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.