MolNFT v1 · #168718 · protein
Pyruvate kinase M2 mutant-S37E K433E
6WP6 · Pyruvate kinase pkm: “Pyruvate kinase M2 mutant-S37E K433E”. X-ray diffraction, 3 ligands (OXL, MG, NO3), 15 pockets (best druggability 0.84). MolNFT v1 #168718 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WP6
- Type
- protein
- Length
- 1,005 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, NO3
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 500 | 39% helix, 20% strand | P14618 |
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 505 | 39% helix, 21% strand | P14618 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · chains C
- MG · Magnesium ion · metal · 2 copies · chains C, A
- NO3 · Nitrate ion · ion · chains C
- GOL · Glycerol · additive · 3 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.84 | 0.88 | 104 | MG, OXL |
| 2 | 432 | 0.80 | 0.88 | 44 | empty |
| 3 | 482 | 0.77 | 0.85 | 62 | MG |
| 4 | 166 | 0.58 | 0.82 | 25 | GOL |
| 5 | 168 | 0.55 | 0.81 | 28 | GOL |
Interfaces
1 interface between chains.
- C–A · 2713 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6WP6 · Pyruvate Kinase M2 mutant-S37E K433E · the same entry in another collection · chain C against C, 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 6WP6 · PDBe 6WP6 · UniProt P14618
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