4RPA | pdb_00004rpa

Crystal structure of inorganic pyrophosphatase from Staphylococcus aureus in complex with Mn2+

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4rpab_	Alpha and beta proteins (a/b)	DHH phosphoesterases	DHH phosphoesterases	Manganese-dependent inorganic pyrophosphatase (family II)	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d4rpaa_	Alpha and beta proteins (a/b)	DHH phosphoesterases	DHH phosphoesterases	Manganese-dependent inorganic pyrophosphatase (family II)	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	DHH phosphoesterases	8066743	3000896	SCOP2B (2022-06-29)
A	SCOP2 Family	Manganese-dependent inorganic pyrophosphatase (family II)	8066742	4003453	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DHH phosphoesterases	8066743	3000896	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)
B	Cas_Cas5d	e4rpaB1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
A	Cas_Cas5d	e4rpaA1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.1640.10	Alpha Beta	Alpha-Beta Complex	inorganic pyrophosphatase (n-terminal core)	inorganic pyrophosphatase (n-terminal core)	CATH (4.3.0)
B	3.10.310.20	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
A	3.90.1640.10	Alpha Beta	Alpha-Beta Complex	inorganic pyrophosphatase (n-terminal core)	inorganic pyrophosphatase (n-terminal core)	CATH (4.3.0)
A	3.10.310.20	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable manganese-dependent inorganic pyrophosphatase	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity inorganic diphosphate phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR022934	Manganese-dependent inorganic pyrophosphatase, probable	Family
A, B	IPR001667	DDH domain	Domain
A, B	IPR004097	DHHA2 domain	Domain
A, B	IPR038763	DHH phosphoesterase superfamily	Homologous Superfamily
A, B	IPR038222	DHHA2 domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210
A, B	OCS	Parent Component: CYS RESID: AA0205 , AA0556 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , L-cysteic acid (L-cysteine sulfonic acid) MOD:00460

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.