MolNFT v1 · #108823 · protein
Human pyruvate kinase M2 mutant C424A
4WJ8 · Pyruvate kinase pkm: “Human pyruvate kinase M2 mutant C424A”. X-ray diffraction, 6 ligands (OXD, FBP, K), 20 pockets (best druggability 0.87). MolNFT v1 #108823 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WJ8
- Type
- protein
- Length
- 2,068 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
- OXD, FBP, K, MG, PO4, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 518 | 39% helix, 20% strand | P14618 |
| B, D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 517 | 39% helix, 20% strand | P14618 |
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 516 | 39% helix, 20% strand | P14618 |
Ligands and binding sites
- OXD · Oxalic acid · ligand · 4 copies · chains A, B, C, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, C
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 5 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 | 357 | 0.87 | 0.95 | 41 | empty |
| 2 | 344 | 0.87 | 0.96 | 44 | empty |
| 3 | 1173 | 0.86 | 0.87 | 123 | empty |
| 4 | 1042 | 0.84 | 0.85 | 135 | OXD, MG, K, GOL |
| 5 | 1084 | 0.84 | 0.85 | 152 | OXD, K, MG, PO4 |
Interfaces
6 interfaces between chains.
- A–C · 3144 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 3124 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1310 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1297 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 60 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4WJ8 · Human Pyruvate Kinase M2 Mutant C424A · 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 4WJ8 · PDBe 4WJ8 · UniProt P14618
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