13PK

TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d13pka_	Alpha and beta proteins (a/b)	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
B	d13pkb_	Alpha and beta proteins (a/b)	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
C	d13pkc_	Alpha and beta proteins (a/b)	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
D	d13pkd_	Alpha and beta proteins (a/b)	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Phosphoglycerate kinase	8033102	3001564	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoglycerate kinase	8033102	3001564	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phosphoglycerate kinase	8033102	3001564	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phosphoglycerate kinase	8033102	3001564	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	PGK_N	e13pkA1	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 1 (From Topology)	H: Phosphoglycerate kinase domain 1 (From Topology)	T: Phosphoglycerate kinase domain 1	F: PGK_N	ECOD (1.6)
A	PGK_C	e13pkA2	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 2 (From Topology)	H: Phosphoglycerate kinase domain 2 (From Topology)	T: Phosphoglycerate kinase domain 2	F: PGK_C	ECOD (1.6)
B	PGK_N	e13pkB2	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 1 (From Topology)	H: Phosphoglycerate kinase domain 1 (From Topology)	T: Phosphoglycerate kinase domain 1	F: PGK_N	ECOD (1.6)
B	PGK_C	e13pkB1	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 2 (From Topology)	H: Phosphoglycerate kinase domain 2 (From Topology)	T: Phosphoglycerate kinase domain 2	F: PGK_C	ECOD (1.6)
C	PGK_N	e13pkC1	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 1 (From Topology)	H: Phosphoglycerate kinase domain 1 (From Topology)	T: Phosphoglycerate kinase domain 1	F: PGK_N	ECOD (1.6)
C	PGK_C	e13pkC2	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 2 (From Topology)	H: Phosphoglycerate kinase domain 2 (From Topology)	T: Phosphoglycerate kinase domain 2	F: PGK_C	ECOD (1.6)
D	PGK_N	e13pkD2	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 1 (From Topology)	H: Phosphoglycerate kinase domain 1 (From Topology)	T: Phosphoglycerate kinase domain 1	F: PGK_N	ECOD (1.6)
D	PGK_C	e13pkD1	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 2 (From Topology)	H: Phosphoglycerate kinase domain 2 (From Topology)	T: Phosphoglycerate kinase domain 2	F: PGK_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate kinase, N-terminal domain	CATH (4.3.0)
B	3.40.50.1260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate kinase, N-terminal domain	CATH (4.3.0)
C	3.40.50.1260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate kinase, N-terminal domain	CATH (4.3.0)
D	3.40.50.1260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate kinase, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00162	Phosphoglycerate kinase (PGK)	Phosphoglycerate kinase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	3-PHOSPHOGLYCERATE KINASE	phosphoglycerate kinase activity kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding phosphoglycerate kinase activity kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 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	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle metabolic process glycolytic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process cellular nitrogen compound metabolic process primary metabolic process purine-containing compound catabolic process aromatic compound catabolic process nucleotide metabolic process cellular nitrogen compound catabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process heterocycle catabolic process nucleoside diphosphate catabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process catabolic process ATP metabolic process purine nucleotide metabolic process organic substance metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process nitrogen compound metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy organic cyclic compound catabolic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process organic substance catabolic process purine ribonucleoside diphosphate catabolic process cellular aromatic compound metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody glycosome cytoplasm cellular anatomical entity intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001576	Phosphoglycerate kinase	Family
A, B, C, D	IPR027250	Phosphoglycerate kinase, euglenozoa	Family
A, B, C, D	IPR015824	Phosphoglycerate kinase, N-terminal	Homologous Superfamily
A, B, C, D	IPR036043	Phosphoglycerate kinase superfamily	Homologous Superfamily
A, B, C, D	IPR015911	Phosphoglycerate kinase, conserved site	Conserved Site

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	phosphoglycerate kinase M-CSA #40	The first energy-producing reaction of glycolysis is catalysed by phosphoglycerate kinase (PGK). This enzyme is unusual among kinases in that, biologically it functions mainly in the reverse (with respect to the EC) direction to phosphorylate ADP. Here we show the biological direction. This important energy saving feature makes it fairly ubiquitous. In all known cases it requires an Mg(II) ion to reduce charge repulsion between the negatively charged phosphate groups, enabling the two charged phosphate groups to interact.	Defined by 4 residues: ARG:A-35 [auth A-39]LYS:A-215 [auth A-219]GLY:A-372 [auth A-376]GLY:A-395 [auth A-399] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.2.3 (PDB Primary Data) Search M-CSA Motif + EC 2.7.2.3

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.