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Crystal structures of leishmania mexicana pyruvate kinase (lmpyk) in complex with ATP and oxalate

Analyse Crystal structures of leishmania mexicana pyruvate kinase (lmpyk) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HQO
Type: protein
Length: 1,964 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase
EC: 2.7.1.40
UniProt: Q27686
Ligands: OXL, ATP, MG, K
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K, A, B, C	Pyruvate kinase (EC 2.7.1.40)	protein	491	39% helix, 22% strand	Q27686

Ligands and binding sites

OXL · Oxalate ion · ligand · 4 copies · chains K, A, B, C
ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains K, A, B, C
MG · Magnesium ion · metal · 6 copies · chains K, A, B, C
K · Potassium ion · metal · 4 copies · chains K, A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1054	0.84	0.85	147	MG, K, OXL, ATP
2	373	0.76	0.86	35	empty
3	556	0.76	0.83	65	MG, K, OXL, ATP
4	540	0.75	0.83	61	MG, K, OXL, ATP
5	962	0.74	0.77	84	empty

Interfaces

5 interfaces between chains.

K–B · 2979 Å² buried · 23 hydrogen bonds · protein-protein
K–C · 590 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 248 Å² buried · 2 hydrogen bonds · protein-protein
K–A · 211 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 155 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3HQO · Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and… · the same entry in another collection · chain K against K, TM-score 1.00
Q27686 · AlphaFold monomer V2.0 prediction for pyruvate kinase (Q27686) · a predicted model of the same protein · chain K against A, TM-score 0.90

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q27686
Elsewhere: RCSB PDB 3HQO · PDBe 3HQO · UniProt Q27686

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