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Crystal structure of M. tuberculosis DprE1 in complex with the non-covalent inhibitor QN118
Analyse Crystal structure of M. tuberculosis DprE1 in complex with the non-covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P8N
- Type
- protein
- Length
- 873 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.79
- Source
- Mycobacterium tuberculosis
- Molecule
- Probable decaprenylphosphoryl-beta-D-ribose oxidase
- EC
- 1.-.-.-
- UniProt
- P72056
- Ligands
- FAD, R57
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.79 · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 454 | 31% helix, 24% strand | P72056 |
| B | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 419 | 32% helix, 26% strand | P72056 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- R57 · 3-[(3-fluoro-4-methoxybenzyl)amino]-6-(trifluoromethyl)quinoxaline-2-carboxylic acid · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.84 | 0.85 | 94 | FAD, R57 |
| 2 | 579 | 0.78 | 0.84 | 69 | FAD, R57 |
| 3 | 685 | 0.67 | 0.75 | 64 | empty |
| 4 | 74 | 0.44 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 489 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4P8N · Crystal structure of M. tuberculosis DPRE1 in complex with the non- covalent inhibitor… · the same entry in another collection · chain A against A, 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 P72056
- Elsewhere: RCSB PDB 4P8N · PDBe 4P8N · UniProt P72056
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