MolNFT v1 · #152793 · protein
Crystal structure of pyruvate kinase (pyk) from mycobacterium tuberculosis in complex with oxalate, AMP and inhibitor ribose 5- phosphate
6ITO: “Crystal structure of pyruvate kinase (pyk) from mycobacterium tuberculosis in complex with oxalate, AMP and…”. X-ray diffraction, 4 ligands (OXL, R5P, AMP), 20 pockets (best druggability 0.74). MolNFT v1 #152793 on GenesisL1: 3D…
- PDB
- 6ITO
- 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, R5P, AMP, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase (EC 2.7.1.40) | protein | 471 | 38% helix, 24% strand | P9WKE5 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- R5P · Ribose-5-phosphate · ligand · 4 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.74 | 0.96 | 28 | AMP |
| 2 | 94 | 0.74 | 0.96 | 28 | AMP |
| 3 | 646 | 0.73 | 0.80 | 74 | OXL |
| 4 | 89 | 0.73 | 0.96 | 28 | AMP |
| 5 | 585 | 0.72 | 0.81 | 76 | MG, OXL |
Interfaces
4 interfaces between chains.
- C–D · 1670 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1649 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1029 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1017 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6ITO · Crystal structure of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex… · 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 6ITO · PDBe 6ITO · UniProt P9WKE5
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