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Pyruvate kinase (pyk) from trypanosoma brucei soaked with D-malate

Analyse Pyruvate kinase (pyk) from trypanosoma brucei soaked with D-malate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KCU
Type: protein
Length: 996 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase 1
EC: 2.7.1.40
UniProt: P30615
Ligands: MLT, FDP, MG, K
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pyruvate kinase 1 (EC 2.7.1.40)	protein	498	41% helix, 22% strand	P30615

Ligands and binding sites

MLT · D-malate · ligand · 2 copies · chains A, B
FDP · 2,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	581	0.78	0.84	68	empty
2	553	0.76	0.83	68	MG, K, MLT
3	537	0.71	0.80	67	MG, K, MLT
4	299	0.59	0.78	32	empty
5	291	0.59	0.78	34	empty

Interfaces

1 interface between chains.

A–B · 2714 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4KCU · Pyruvate kinase (PYK) from Trypanosoma brucei soaked with D-Malate · the same entry in another collection · chain A against A, TM-score 1.00
P30615 · AlphaFold monomer V2.0 prediction for pyruvate kinase 1 (P30615) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P30615
Elsewhere: RCSB PDB 4KCU · PDBe 4KCU · UniProt P30615

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