MolNFT v1 · #22439 · protein

Human pyruvate kinase M2

1T5A · Pyruvate kinase, M2 isozyme: “Human pyruvate kinase M2”. X-ray diffraction, 5 ligands (FBP, OXL, MG), 20 pockets (best druggability 0.86). MolNFT v1 #22439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1T5A
Type: protein
Length: 2,076 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase, M2 isozyme
EC: 2.7.1.40
UniProt: P14618
Ligands: FBP, OXL, MG, K, PO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Pyruvate kinase, M2 isozyme (EC 2.7.1.40)	protein	519	40% helix, 21% strand	P14618

Ligands and binding sites

FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
K · Potassium ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 20 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	341	0.86	0.96	40	empty
2	340	0.86	0.96	40	empty
3	526	0.86	0.93	36	empty
4	646	0.79	0.85	92	OXL, PO4, MG, K, GOL
5	730	0.78	0.83	92	OXL, PO4, MG, K, GOL

Interfaces

6 interfaces between chains.

B–D · 3006 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 2995 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1265 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1240 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 61 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1T5A · Human Pyruvate Kinase M2 · the same entry in another collection · chain A against A, TM-score 1.00
P14618 · AlphaFold monomer V2.0 prediction for pyruvate kinase pkm (P14618) · a predicted model of the same protein · chain A against A, 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 P14618
Elsewhere: RCSB PDB 1T5A · PDBe 1T5A · UniProt P14618

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