3HQO

Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and Oxalate

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth K]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043649	3000510	SCOP2B (2022-06-29)
A [auth K]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043649	3000510	SCOP2B (2022-06-29)
A [auth K]	SCOP2B Superfamily	PK beta-barrel domain-like	8042557	3001296	SCOP2B (2022-06-29)
A [auth K]	SCOP2B Superfamily	PK C-terminal domain-like	8044406	3000442	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	PK beta-barrel domain-like	8042557	3001296	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043649	3000510	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	PK C-terminal domain-like	8044406	3000442	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043649	3000510	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	PK C-terminal domain-like	8044406	3000442	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043649	3000510	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043649	3000510	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	PK beta-barrel domain-like	8042557	3001296	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043649	3000510	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	PK beta-barrel domain-like	8042557	3001296	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043649	3000510	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	PK C-terminal domain-like	8044406	3000442	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 [auth K]	PK_2nd	e3hqoK4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
A [auth K]	PK_1st	e3hqoK2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
A [auth K]	PK_C	e3hqoK1	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
B [auth A]	PK_2nd	e3hqoA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
B [auth A]	PK_1st	e3hqoA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
B [auth A]	PK_C	e3hqoA1	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
C [auth B]	PK_2nd	e3hqoB4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
C [auth B]	PK_1st	e3hqoB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
C [auth B]	PK_C	e3hqoB1	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
D [auth C]	PK_2nd	e3hqoC4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
D [auth C]	PK_1st	e3hqoC2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
D [auth C]	PK_C	e3hqoC1	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth K]	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
A [auth K]	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
A [auth K]	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
B [auth A]	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
B [auth A]	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
B [auth A]	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
C [auth B]	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
C [auth B]	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
C [auth B]	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
D [auth C]	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
D [auth C]	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
D [auth C]	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth K], B [auth A], C [auth B], D [auth C]	PF02887	Pyruvate kinase, alpha/beta domain (PK_C)	Pyruvate kinase, alpha/beta domain	Pyruvate kinase catalyses the final step in glycolysis, the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP [1,2]. The structure of several pyruvate kinases from various organisms have been determined [2, ...	Pyruvate kinase catalyses the final step in glycolysis, the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP [1,2]. The structure of several pyruvate kinases from various organisms have been determined [2, 3,4]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain (represented in this entry). This domain is at the C-terminal of pyruvate kinases and contains the FBP (fructose 1,6-bisphosphate) binding site [2,4,5].	Domain
A [auth K], B [auth A], C [auth B], D [auth C]	PF00224	Pyruvate kinase, barrel domain (PK)	Pyruvate kinase, barrel domain	This is the barrel domain of pyruvate kinases. This domain represents the beta/alpha barrel and the small beta-barrel domain inserted within it. The active site is found in a cleft between the two domains [1,2,3,4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth K], B [auth A], C [auth B], D [auth C]	Pyruvate kinase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding potassium ion binding alkali metal ion binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups pyruvate kinase activity phosphotransferase activity, alcohol group as acceptor	-	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth K], B [auth A], C [auth B], D [auth C]	IPR015795	Pyruvate kinase, C-terminal	Domain
A [auth K], B [auth A], C [auth B], D [auth C]	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A [auth K], B [auth A], C [auth B], D [auth C]	IPR011037	Pyruvate kinase-like, insert domain superfamily	Homologous Superfamily
A [auth K], B [auth A], C [auth B], D [auth C]	IPR015806	Pyruvate kinase, insert domain superfamily	Homologous Superfamily
A [auth K], B [auth A], C [auth B], D [auth C]	IPR036918	Pyruvate kinase, C-terminal domain superfamily	Homologous Superfamily
A [auth K], B [auth A], C [auth B], D [auth C]	IPR001697	Pyruvate kinase	Family
A [auth K], B [auth A], C [auth B], D [auth C]	IPR018209	Pyruvate kinase, active site	Active Site
A [auth K], B [auth A], C [auth B], D [auth C]	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A [auth K], B [auth A], C [auth B], D [auth C]	IPR015793	Pyruvate kinase, barrel	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.