Research workbench

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: 3BJT
Type: protein
Length: 2,048 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: OXL, MG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 38% 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	512	38% helix, 21% strand	P14618

Ligands and binding sites

OXL · Oxalate ion · ligand · 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	355	0.86	0.95	53	empty
2	345	0.86	0.95	42	empty
3	978	0.86	0.87	66	empty
4	1177	0.84	0.85	157	OXL, MG
5	534	0.79	0.86	81	OXL, MG

Interfaces

6 interfaces between chains.

B–D · 3048 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 3025 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 1267 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1229 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 52 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3BJT · Pyruvate kinase M2 is a phosphotyrosine binding protein · 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 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 3BJT · PDBe 3BJT · UniProt P14618

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.