MolNFT v1 · #104620 · protein
Crystal structure of PKM2-Y105E mutant
4QG6 · Pyruvate kinase pkm: “Crystal structure of PKM2-Y105E mutant”. X-ray diffraction, 1 ligand (PRO), 20 pockets (best druggability 0.83). MolNFT v1 #104620 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QG6
- Type
- protein
- Length
- 1,819 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
- PRO
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 406 | 45% helix, 15% strand | P14618 |
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 502 | 37% helix, 18% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 505 | 39% helix, 18% strand | P14618 |
Ligands and binding sites
- PRO · Proline · ligand · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.83 | 0.87 | 85 | empty |
| 2 | 652 | 0.82 | 0.86 | 71 | empty |
| 3 | 878 | 0.73 | 0.77 | 93 | empty |
| 4 | 803 | 0.72 | 0.78 | 78 | empty |
| 5 | 448 | 0.67 | 0.79 | 56 | PRO |
Interfaces
4 interfaces between chains.
- B–C · 2499 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 2485 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1354 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1325 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
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 4QG6 · PDBe 4QG6 · UniProt P14618
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