Research workbench
T-state crystal structure of pyruvate kinase from mycobacterium tuberculosis
Analyse T-state crystal structure of pyruvate kinase from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WRP
- Type
- protein
- Length
- 1,796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- P9WKE5
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pyruvate kinase (EC 2.7.1.40) | protein | 473 | 38% helix, 23% strand | P9WKE5 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 472 | 38% helix, 24% strand | P9WKE5 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 378 | 46% helix, 18% strand | P9WKE5 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 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 | 826 | 0.74 | 0.79 | 79 | empty |
| 2 | 886 | 0.74 | 0.78 | 77 | empty |
| 3 | 620 | 0.72 | 0.79 | 54 | empty |
| 4 | 173 | 0.63 | 0.85 | 29 | PO4 |
| 5 | 240 | 0.61 | 0.81 | 26 | PO4 |
Interfaces
4 interfaces between chains.
- A–B · 1211 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1171 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1134 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1096 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5WRP · T-state crystal structure of pyruvate kinase from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
- P9WKE5 · AlphaFold monomer V2.0 prediction for pyruvate kinase (P9WKE5) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P9WKE5
- Elsewhere: RCSB PDB 5WRP · PDBe 5WRP · UniProt P9WKE5
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