MolNFT v1 · #166976 · protein

Crystal structure of human PKM2 in complex with L-asparagine

6V74 · Pyruvate kinase pkm: “Crystal structure of human PKM2 in complex with L-asparagine”. X-ray diffraction, 6 ligands (OXL, FBP, ASN), 20 pockets (best druggability 0.86). MolNFT v1 #166976 on GenesisL1: 3D structure, binding sites and…

PDB: 6V74
Type: protein
Length: 1,955 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase pkm
EC: 2.7.1.40
UniProt: P14618
Ligands: OXL, FBP, ASN, K, MG, CL
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate kinase pkm (EC 2.7.1.40)	protein	513	39% helix, 20% strand	P14618
B	Pyruvate kinase pkm (EC 2.7.1.40)	protein	516	39% helix, 21% strand	P14618
C	Pyruvate kinase pkm (EC 2.7.1.40)	protein	499	41% helix, 16% strand	P14618
D	Pyruvate kinase pkm (EC 2.7.1.40)	protein	427	46% helix, 16% strand	P14618

Ligands and binding sites

OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
ASN · Asparagine · ligand · chains C
K · Potassium ion · metal · 4 copies · chains A, C
MG · Magnesium ion · metal · 4 copies · chains A, B, D
CL · Chloride ion · ion · 2 copies · chains B, C
GOL · Glycerol · additive · 17 copies · chains A, B, C, D
144 · Tris-hydroxymethyl-methyl-ammonium · additive · chains 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	310	0.86	0.96	40	GOL
2	1012	0.79	0.81	128	K, GOL, OXL
3	655	0.74	0.81	72	K, GOL, OXL, MG
4	618	0.74	0.81	71	CL, GOL, OXL, MG
5	83	0.68	0.93	26	empty

Interfaces

5 interfaces between chains.

A–C · 2694 Å² buried · 36 hydrogen bonds · protein-protein
A–D · 202 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 194 Å² buried · 1 hydrogen bond · protein-protein
B–C · 189 Å² buried · 1 hydrogen bond · protein-protein
A–B · 55 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6V74 · Crystal Structure of Human PKM2 in Complex with L-asparagine · the same entry in another collection · chain D against D, TM-score 1.00
P14618 · AlphaFold monomer V2.0 prediction for pyruvate kinase pkm (P14618) · a predicted model of the same protein · chain D 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 6V74 · PDBe 6V74 · UniProt P14618

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