MolNFT v1 · #365 · protein

Bis mg-ATP-K-oxalate complex of pyruvate kinase

1A49: “Bis mg-ATP-K-oxalate complex of pyruvate kinase”. X-ray diffraction, 4 ligands (OXL, ATP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #365 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1A49
Type: protein
Length: 4,152 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase
EC: 2.7.1.40
UniProt: P11974
Ligands: OXL, ATP, MG, K
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Pyruvate kinase (EC 2.7.1.40)	protein	519	39% helix, 20% strand	P11974

Ligands and binding sites

OXL · Oxalate ion · ligand · 8 copies · chains A, B, C, D, E, F, G, H
ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, C, D, E, F, G
MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H
K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1056	0.89	0.91	98	empty
2	1151	0.88	0.90	105	empty
3	342	0.86	0.95	42	empty
4	355	0.86	0.95	47	empty
5	1064	0.86	0.87	128	K, OXL, MG, ATP

Interfaces

13 interfaces between chains.

A–C · 3068 Å² buried · 40 hydrogen bonds · protein-protein
E–G · 3023 Å² buried · 34 hydrogen bonds · protein-protein
F–H · 2973 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 2920 Å² buried · 44 hydrogen bonds · protein-protein
G–H · 1413 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1A49 · Bis mg-ATP-K-oxalate complex of pyruvate kinase · the same entry in another collection · chain G against G, TM-score 1.00
P11974 · AlphaFold monomer V2.0 prediction for pyruvate kinase pkm (P11974) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P11974
Elsewhere: RCSB PDB 1A49 · PDBe 1A49 · UniProt P11974

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