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Crystal structure of leishmania mexicana pyruvate kinase (lmpyk) in complex with ATP, oxalate and fructose 2,6 bisphosphate

Analyse Crystal structure 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: 3HQP
Type: protein
Length: 7,968 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase
EC: 2.7.1.40
UniProt: Q27686
Ligands: FDP, OXL, ATP, K, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	Pyruvate kinase (EC 2.7.1.40)	protein	498	39% helix, 20% strand	Q27686

Ligands and binding sites

FDP · 2,6-di-O-phosphono-beta-D-fructofuranose · ligand · 16 copies · chains A, B, C, D, I, E, F, G, H, J, K, L, M, N, O, P
OXL · Oxalate ion · ligand · 15 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, P
ATP · Adenosine-5'-triphosphate · ligand · 15 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, P
K · Potassium ion · metal · 32 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
MG · Magnesium ion · metal · 30 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, P
GOL · Glycerol · additive · 6 copies · chains E, G, H, I, J, O

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.85	0.86	142	MG, K, OXL, ATP
2	1140	0.84	0.85	142	MG, K, OXL, ATP
3	1154	0.82	0.84	141	MG, K, OXL, ATP, GOL
4	820	0.82	0.85	109	MG, K, OXL, ATP
5	1117	0.82	0.83	136	MG, K, OXL, ATP

Interfaces

27 interfaces between chains.

N–P · 3027 Å² buried · 23 hydrogen bonds · protein-protein
F–H · 2962 Å² buried · 24 hydrogen bonds · protein-protein
M–O · 2950 Å² buried · 22 hydrogen bonds · protein-protein
J–L · 2946 Å² buried · 25 hydrogen bonds · protein-protein
I–K · 2933 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

3HQP · Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP… · the same entry in another collection · chain P against P, TM-score 1.00

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 3HQP · PDBe 3HQP · UniProt Q27686

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