MolNFT v1 · #158453 · protein

Pyruvate kinase M2 mutant - S437Y in complex with L-serine

6NUB · Pyruvate kinase pkm: “Pyruvate kinase M2 mutant - S437Y in complex with L-serine”. X-ray diffraction, 5 ligands (SER, OXL, MG), 18 pockets (best druggability 0.86). MolNFT v1 #158453 on GenesisL1: 3D structure, binding sites and…

PDB: 6NUB
Type: protein
Length: 1,041 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase pkm
EC: 2.7.1.40
UniProt: P14618
Ligands: SER, OXL, MG, K, SCN
Pockets: 18 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate kinase pkm (EC 2.7.1.40)	protein	522	39% helix, 20% strand	P14618
B	Pyruvate kinase pkm (EC 2.7.1.40)	protein	519	39% helix, 20% strand	P14618

Ligands and binding sites

SER · Serine · ligand · 2 copies · chains A, B
OXL · Oxalate ion · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B
SCN · Thiocyanate ion · ion · 5 copies · chains A, B
B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A
PG4 · Tetraethylene glycol · additive · chains A, B
EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	344	0.86	0.96	46	PG4, EDO
2	481	0.75	0.84	59	MG, OXL, K, B3P
3	435	0.74	0.84	55	MG, OXL, B3P
4	160	0.59	0.83	28	SER
5	166	0.56	0.81	28	SER

Interfaces

1 interface between chains.

A–B · 3018 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

6NUB · Pyruvate Kinase M2 Mutant - S437Y in Complex with L-serine · the same entry in another collection · chain B against B, 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 6NUB · PDBe 6NUB · UniProt P14618

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