Research workbench
Pyruvate kinase (pyk) from mycobacterium tuberculosis in complex with oxalate and allosteric activator glucose 6-phosphate
Analyse Pyruvate kinase (pyk) from mycobacterium tuberculosis in complex with oxalate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WSA
- Type
- protein
- Length
- 1,884 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
- OXL, G6P, MG, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase (EC 2.7.1.40) | protein | 471 | 37% helix, 24% strand | P9WKE5 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.81 | 0.82 | 118 | MG, OXL |
| 2 | 1123 | 0.80 | 0.82 | 130 | MG, OXL |
| 3 | 90 | 0.72 | 0.95 | 27 | PO4 |
| 4 | 100 | 0.71 | 0.94 | 28 | PO4 |
| 5 | 85 | 0.70 | 0.94 | 25 | PO4 |
Interfaces
4 interfaces between chains.
- C–D · 1791 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1702 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1028 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1014 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5WSA · Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate and… · 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 A against A, TM-score 0.97
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 5WSA · PDBe 5WSA · UniProt P9WKE5
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