MolNFT v1 · #104623 · protein
Crystal structure of PKM2-R399E mutant
4QG9 · Pyruvate kinase pkm: “Crystal structure of PKM2-R399E mutant”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.87). MolNFT v1 #104623 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QG9
- Type
- protein
- Length
- 1,824 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
- MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 499 | 40% helix, 20% strand | P14618 |
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 503 | 40% helix, 21% strand | P14618 |
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 417 | 47% helix, 15% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 405 | 47% helix, 16% strand | P14618 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- ACT · Acetate ion · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.87 | 0.94 | 51 | empty |
| 2 | 351 | 0.86 | 0.95 | 44 | empty |
| 3 | 937 | 0.74 | 0.78 | 83 | MG |
| 4 | 516 | 0.69 | 0.79 | 48 | MG |
| 5 | 429 | 0.63 | 0.77 | 48 | MG |
Interfaces
5 interfaces between chains.
- A–D · 2567 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2432 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1009 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 921 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QG9 · crystal structure of PKM2-R399E 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 4QG9 · PDBe 4QG9 · UniProt P14618
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