6PHT

Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 5-[(3-aminopropyl)amino]pentylboronic acid

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	d6phta1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	automated matches	automated matches	(Marinobacter subterrani ) [TaxId: 1658765 ],	SCOPe (2.08)
A	d6phta2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Marinobacter subterrani ) [TaxId: 1658765 ],	SCOPe (2.08)
B	d6phtb1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	automated matches	automated matches	(Marinobacter subterrani ) [TaxId: 1658765 ],	SCOPe (2.08)
B	d6phtb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Marinobacter subterrani ) [TaxId: 1658765 ],	SCOPe (2.08)
C	d6phtc1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	automated matches	automated matches	(Marinobacter subterrani ) [TaxId: 1658765 ],	SCOPe (2.08)
C	d6phtc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Marinobacter subterrani ) [TaxId: 1658765 ],	SCOPe (2.08)
D	d6phtd1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	automated matches	automated matches	(Marinobacter subterrani ) [TaxId: 1658765 ],	SCOPe (2.08)
D	d6phtd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Marinobacter subterrani ) [TaxId: 1658765 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	HDAC-like	8101214	4000427	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arginase/deacetylase-like	8101215	3000260	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8101215	3000260	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Arginase/deacetylase-like	8101215	3000260	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Arginase/deacetylase-like	8101215	3000260	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	Hist_deacetyl	e6phtA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
B	Hist_deacetyl	e6phtB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
C	Hist_deacetyl	e6phtC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
D	Hist_deacetyl	e6phtD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (utative)
B	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (utative)
C	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (utative)
D	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00850	Histone deacetylase domain (Hist_deacetyl)	Histone deacetylase domain	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Acetylpolyamine amidohydrolase	cation binding ion binding binding metal ion binding small molecule binding deacetylase activity histone deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity histone modifying activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000286	Histone deacetylase family	Family
A, B, C, D	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
A, B, C, D	IPR023801	Histone deacetylase domain	Domain
A, B, C, D	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A, B, C, D	IPR050284	Histone deacetylase and polyamine deacetylase	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.