3EK6

Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium

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	d3ek6a1	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
A	d3ek6a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
B	d3ek6b_	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
C	d3ek6c_	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
D	d3ek6d_	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
E	d3ek6e_	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
F	d3ek6f_	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Carbamate kinase-like	8074976	3001310	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Carbamate kinase-like	8074976	3001310	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Carbamate kinase-like	8074976	3001310	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Carbamate kinase-like	8074976	3001310	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Carbamate kinase-like	8074976	3001310	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Carbamate kinase-like	8074976	3001310	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	PF00696	e3ek6A1	A: a/b three-layered sandwiches	X: Carbamate kinase-like (From Topology)	H: Carbamate kinase-like (From Topology)	T: Carbamate kinase-like	F: PF00696	ECOD (1.6)
B	PF00696	e3ek6B1	A: a/b three-layered sandwiches	X: Carbamate kinase-like (From Topology)	H: Carbamate kinase-like (From Topology)	T: Carbamate kinase-like	F: PF00696	ECOD (1.6)
C	PF00696	e3ek6C1	A: a/b three-layered sandwiches	X: Carbamate kinase-like (From Topology)	H: Carbamate kinase-like (From Topology)	T: Carbamate kinase-like	F: PF00696	ECOD (1.6)
D	PF00696	e3ek6D1	A: a/b three-layered sandwiches	X: Carbamate kinase-like (From Topology)	H: Carbamate kinase-like (From Topology)	T: Carbamate kinase-like	F: PF00696	ECOD (1.6)
E	PF00696	e3ek6E1	A: a/b three-layered sandwiches	X: Carbamate kinase-like (From Topology)	H: Carbamate kinase-like (From Topology)	T: Carbamate kinase-like	F: PF00696	ECOD (1.6)
F	PF00696	e3ek6F1	A: a/b three-layered sandwiches	X: Carbamate kinase-like (From Topology)	H: Carbamate kinase-like (From Topology)	T: Carbamate kinase-like	F: PF00696	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
B	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
C	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
D	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
E	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
F	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	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	PF00696	Amino acid kinase family (AA_kinase)	Amino acid kinase family	-	Family

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	Uridylate kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nucleobase-containing compound kinase activity UMP kinase activity nucleoside monophosphate kinase activity kinase activity transferase activity catalytic activity UMP/dUMP kinase activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process ribose phosphate metabolic process pyrimidine nucleoside diphosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process UDP metabolic process nucleobase-containing compound metabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process ribose phosphate metabolic process pyrimidine nucleoside diphosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process UDP metabolic process nucleobase-containing compound metabolic process nucleoside diphosphate biosynthetic process ribonucleotide biosynthetic process organic substance metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process pyrimidine ribonucleoside diphosphate metabolic process ribonucleoside diphosphate metabolic process organic substance biosynthetic process small molecule metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process organonitrogen compound metabolic process primary metabolic process pyrimidine ribonucleoside diphosphate biosynthetic process nucleobase-containing compound biosynthetic process nucleotide metabolic process organic cyclic compound metabolic process nucleoside diphosphate metabolic process UDP biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process pyrimidine nucleoside diphosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleotide biosynthetic process ribonucleoside diphosphate biosynthetic process pyrimidine ribonucleotide biosynthetic process CTP biosynthetic process 'de novo' CTP biosynthetic process pyrimidine ribonucleoside triphosphate biosynthetic process pyrimidine nucleoside triphosphate biosynthetic process ribonucleoside triphosphate metabolic process pyrimidine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process CTP metabolic process ribonucleoside triphosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process nucleoside triphosphate metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR011817	Uridylate kinase	Family
A, B, C, D, E A, B, C, D, E, F	IPR015963	Uridylate kinase, bacteria	Family
A, B, C, D, E A, B, C, D, E, F	IPR001048	Aspartate/glutamate/uridylate kinase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036393	Acetylglutamate kinase-like superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.