Research workbench
Pyruvate kinase M2 mutant-S37E
Analyse Pyruvate kinase M2 mutant-S37E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WP4
- Type
- protein
- Length
- 2,032 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
- OXL, K, MG, PO4, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 511 | 39% helix, 21% strand | P14618 |
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 504 | 39% helix, 22% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 506 | 40% helix, 21% strand | P14618 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 2 copies · chains A, D
- K · Potassium ion · metal · 5 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains C
- GOL · Glycerol · additive · 18 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.86 | 0.95 | 46 | empty |
| 2 | 379 | 0.86 | 0.95 | 41 | empty |
| 3 | 651 | 0.78 | 0.83 | 79 | PO4, MG, K, OXL, GOL |
| 4 | 515 | 0.76 | 0.84 | 63 | MG, K, GOL |
| 5 | 777 | 0.76 | 0.81 | 87 | MG, GOL |
Interfaces
3 interfaces between chains.
- A–C · 2947 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2886 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 739 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6WP4 · Pyruvate Kinase M2 mutant-S37E · 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 6WP4 · PDBe 6WP4 · UniProt P14618
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