MolNFT v1 · #6150 · protein

Recombinant rabbit muscle pyruvate kinase

1F3W: “Recombinant rabbit muscle pyruvate kinase”. X-ray diffraction, 3 ligands (PYR, K, MN), 20 pockets (best druggability 0.88). MolNFT v1 #6150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1F3W
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: PYR, K, MN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 19% 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	40% helix, 19% strand	P11974

Ligands and binding sites

PYR · Pyruvic acid · ligand · 8 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
MN · Manganese (II) 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	504	0.88	0.94	44	empty
2	494	0.88	0.94	46	empty
3	500	0.87	0.94	43	empty
4	503	0.87	0.93	45	empty
5	1079	0.83	0.85	153	K, MN, PYR

Interfaces

15 interfaces between chains.

E–G · 2884 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 2857 Å² buried · 28 hydrogen bonds · protein-protein
F–H · 2846 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 2785 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 1312 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

1F3W · Recombinant rabbit muscle pyruvate kinase · the same entry in another collection · chain H against H, 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 0.99

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 P11974
Elsewhere: RCSB PDB 1F3W · PDBe 1F3W · UniProt P11974

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