Research workbench
Pyruvate kinase (pyk) from mycobacterium tuberculosis in complex with oxalate
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
- 5WS8
- Type
- protein
- Length
- 1,856 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, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase (EC 2.7.1.40) | protein | 464 | 38% helix, 23% strand | P9WKE5 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.82 | 0.84 | 166 | MG, OXL |
| 2 | 1123 | 0.82 | 0.83 | 155 | MG, OXL |
| 3 | 57 | 0.62 | 0.92 | 18 | empty |
| 4 | 274 | 0.56 | 0.77 | 31 | empty |
| 5 | 278 | 0.55 | 0.77 | 31 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1650 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1649 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 888 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 880 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5WS8 · Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate · 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 5WS8 · PDBe 5WS8 · UniProt P9WKE5
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