3MEN | pdb_00003men

Crystal structure of acetylpolyamine aminohydrolase from Burkholderia pseudomallei, iodide soak

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3mend1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
D	d3mend2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
C	d3menc1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
C	d3menc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
B	d3menb1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
B	d3menb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
A	d3mena1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
A	d3mena2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Arginase/deacetylase-like	8102172	3000260	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Arginase/deacetylase-like	8102172	3000260	SCOP2B (2022-06-29)
B	SCOP2 Family	HDAC-like	8102171	4000427	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Arginase/deacetylase-like	8102172	3000260	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Arginase/deacetylase-like	8102172	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)
D	Hist_deacetyl	e3menD1	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	e3menC1	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	e3menB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
A	Hist_deacetyl	e3menA2	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)
D	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.2.0)
C	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.2.0)
B	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.2.0)
A	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Acetylpolyamine aminohydrolase	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 deacylase activity histone modifying activity catalytic activity acetylputrescine deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 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 deacylase activity histone modifying activity catalytic activity acetylputrescine deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling cellular process regulation of macromolecule biosynthetic process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050284	HDAC_PDAC	Unknown
A, B, C, D	IPR000286	Histone deacetylase HDAC	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

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.