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Pyruvate kinase M2 is a phosphotyrosine binding protein

Analyse Pyruvate kinase M2 is a phosphotyrosine binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BJF
Type: protein
Length: 2,072 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase isozymes M1/M2
EC: 2.7.1.40
UniProt: P14618
Ligands: FBP, OXL, K, MG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40)	protein	518	39% 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
K · Potassium ion · metal · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 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	604	0.86	0.91	36	empty
2	330	0.86	0.95	42	empty
3	318	0.86	0.95	42	empty
4	633	0.80	0.85	85	OXL, K, MG
5	501	0.78	0.85	65	OXL, K, MG

Interfaces

6 interfaces between chains.

B–D · 2995 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 2984 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 1315 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1264 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 48 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3BJF · Pyruvate kinase M2 is a phosphotyrosine binding protein · the same entry in another collection · chain C against C, 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 0.99

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 3BJF · PDBe 3BJF · UniProt P14618

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