MolNFT v1 · #104626 · protein
Crystal structure of PKM2-K422R mutant
4QGC · Pyruvate kinase pkm: “Crystal structure of PKM2-K422R mutant”. X-ray diffraction, 2 ligands (K, SO4), 20 pockets (best druggability 0.87). MolNFT v1 #104626 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QGC
- Type
- protein
- Length
- 2,000 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
- K, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 503 | 39% helix, 21% strand | P14618 |
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 499 | 39% helix, 19% strand | P14618 |
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 498 | 39% helix, 21% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 500 | 38% helix, 19% strand | P14618 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.87 | 0.95 | 53 | empty |
| 2 | 413 | 0.86 | 0.94 | 43 | empty |
| 3 | 1000 | 0.79 | 0.81 | 97 | K |
| 4 | 732 | 0.76 | 0.81 | 88 | K |
| 5 | 548 | 0.76 | 0.83 | 62 | K, SO4 |
Interfaces
4 interfaces between chains.
- B–C · 2577 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 2567 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1169 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1106 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4QGC · crystal structure of PKM2-K422R mutant · 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 4QGC · PDBe 4QGC · UniProt P14618
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