MolNFT v1 · #168715 · protein
Pyruvate kinase M2 mutant-K433Q
6WP3 · Pyruvate kinase pkm: “Pyruvate kinase M2 mutant-K433Q”. X-ray diffraction, 5 ligands (OXL, MG, K), 14 pockets (best druggability 0.86). MolNFT v1 #168715 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WP3
- Type
- protein
- Length
- 938 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
- OXL, MG, K, NO3, CL
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 510 | 40% helix, 20% strand | P14618 |
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 428 | 46% helix, 15% strand | P14618 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.86 | 0.96 | 40 | NO3 |
| 2 | 740 | 0.76 | 0.81 | 85 | GOL, OXL, MG |
| 3 | 393 | 0.62 | 0.77 | 54 | GOL, OXL, MG, K |
| 4 | 183 | 0.60 | 0.82 | 27 | GOL |
| 5 | 91 | 0.56 | 0.86 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 2796 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6WP3 · Pyruvate Kinase M2 Mutant-K433Q · the same entry in another collection · chain A 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 6WP3 · PDBe 6WP3 · UniProt P14618
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