1KHD | pdb_00001khd

Crystal Structure Analysis of the anthranilate phosphoribosyltransferase from Erwinia carotovora at 1.9 resolution (current name, Pectobacterium carotovorum)

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	d1khdd1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Anthranilate phosphoribosyltransferase (TrpD)	(Pectobacterium carotovorum ) [TaxId: 554 ],	SCOPe (2.08)
D	d1khdd2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Anthranilate phosphoribosyltransferase (TrpD)	(Pectobacterium carotovorum ) [TaxId: 554 ],	SCOPe (2.08)
C	d1khdc1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Anthranilate phosphoribosyltransferase (TrpD)	(Pectobacterium carotovorum ) [TaxId: 554 ],	SCOPe (2.08)
C	d1khdc2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Anthranilate phosphoribosyltransferase (TrpD)	(Pectobacterium carotovorum ) [TaxId: 554 ],	SCOPe (2.08)
B	d1khdb1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Anthranilate phosphoribosyltransferase (TrpD)	(Pectobacterium carotovorum ) [TaxId: 554 ],	SCOPe (2.08)
B	d1khdb2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Anthranilate phosphoribosyltransferase (TrpD)	(Pectobacterium carotovorum ) [TaxId: 554 ],	SCOPe (2.08)
A	d1khda1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Anthranilate phosphoribosyltransferase (TrpD)	(Pectobacterium carotovorum ) [TaxId: 554 ],	SCOPe (2.08)
A	d1khda2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Anthranilate phosphoribosyltransferase (TrpD)	(Pectobacterium carotovorum ) [TaxId: 554 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	8042762	3001630	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	8042759	3000348	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	8042759	3000348	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	8042762	3001630	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	8042762	3001630	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	8042759	3000348	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	8042762	3001630	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	8042759	3000348	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	GatB_Yqey	e1khdD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: GatB_Yqey	ECOD (v294.1)
D	Pribosyltran	e1khdD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)
C	GatB_Yqey	e1khdC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: GatB_Yqey	ECOD (v294.1)
C	Pribosyltran	e1khdC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)
B	GatB_Yqey	e1khdB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: GatB_Yqey	ECOD (v294.1)
B	Pribosyltran	e1khdB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)
A	Glycos_trans_3N	e1khdA1	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N	H: Nucleoside phosphorylase/phosphoribosyltransferase-N	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (v294.1)
A	Pribosyltran	e1khdA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.970.10	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
D	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
C	1.20.970.10	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
C	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
B	1.20.970.10	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
B	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
A	1.20.970.10	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
A	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Anthranilate phosphoribosyltransferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pentosyltransferase activity glycosyltransferase activity transferase activity anthranilate phosphoribosyltransferase activity catalytic activity	oxoacid metabolic process indole-containing compound metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process biogenic amine biosynthetic process indole-containing compound biosynthetic process L-tryptophan metabolic process small molecule metabolic process indolalkylamine biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process oxoacid metabolic process indole-containing compound metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process biogenic amine biosynthetic process indole-containing compound biosynthetic process L-tryptophan metabolic process small molecule metabolic process indolalkylamine biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process L-tryptophan biosynthetic process proteinogenic amino acid metabolic process amine metabolic process amino acid biosynthetic process biosynthetic process amine biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process biogenic amine metabolic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR035902	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily	Homologous Superfamily
A, B, C, D	IPR036320	Glycosyl transferase family 3, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR000312	Glycosyl transferase, family 3	Domain
A, B, C, D	IPR005940	Anthranilate phosphoribosyl transferase	Family
A, B, C, D	IPR017459	Glycosyl transferase family 3, N-terminal domain	Domain

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.