Research workbench
Crystal structure of M. tuberculosis DPRE1 in complex with the non- covalent inhibitor QN114
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
- 4P8M
- Type
- protein
- Length
- 833 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable decaprenylphosphoryl-beta-D-ribose oxidase
- EC
- 1.-.-.-
- UniProt
- P72056
- Ligands
- FAD, R58, 2J3
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 427 | 30% helix, 26% strand | P72056 |
| B | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 406 | 29% helix, 27% strand | P72056 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- R58 · 3-[(4-ethoxybenzyl)amino]-6-(trifluoromethyl)quinoxaline-2-carboxylic acid · ligand · 2 copies · chains A, B
- 2J3 · (2R)-2-{[(2R)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol · ligand · chains A
- IMD · Imidazole · additive · chains A
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 | 770 | 0.80 | 0.84 | 87 | FAD, R58 |
| 2 | 604 | 0.78 | 0.84 | 67 | FAD, R58 |
| 3 | 708 | 0.65 | 0.74 | 74 | empty |
| 4 | 169 | 0.47 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 295 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4P8M · Crystal structure of M. tuberculosis DprE1 in complex with the non-covalent inhibitor… · the same entry in another collection · chain B against B, 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 4P8M · PDBe 4P8M · UniProt P72056
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