Research workbench
Pyruvate kinase M2 mutant-S37D
Analyse Pyruvate kinase M2 mutant-S37D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WP5
- Type
- protein
- Length
- 1,934 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, FBP, K, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 510 | 38% helix, 21% strand | P14618 |
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 510 | 38% helix, 21% strand | P14618 |
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 507 | 39% helix, 21% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 407 | 47% helix, 16% strand | P14618 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 4 copies · chains B, A, C, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 3 copies · chains B, A, D
- K · Potassium ion · metal · 4 copies · chains B, A, C
- MG · Magnesium ion · metal · 3 copies · chains B, A, C
- GOL · Glycerol · additive · 9 copies · chains B, A, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.87 | 0.95 | 52 | empty |
| 2 | 369 | 0.86 | 0.95 | 44 | empty |
| 3 | 1138 | 0.83 | 0.84 | 124 | K, GOL, MG, OXL |
| 4 | 452 | 0.71 | 0.82 | 61 | K, GOL, MG, OXL |
| 5 | 192 | 0.64 | 0.84 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2924 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 2854 Ų buried · 39 hydrogen bonds · protein-protein
- B–A · 697 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6WP5 · Pyruvate Kinase M2 mutant-S37D · the same entry in another collection · chain B against B, 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 6WP5 · PDBe 6WP5 · UniProt P14618
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