Research workbench
Crystal structure of M. tuberculosis DPRE1 in complex with SPBTZ169 (sulfonylpbtz)
Analyse Crystal structure of M. tuberculosis DPRE1 in complex with SPBTZ169… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G83
- Type
- protein
- Length
- 837 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decaprenylphosphoryl-beta-D-ribose oxidase
- EC
- 1.1.98.3
- UniProt
- P9WJF0
- Ligands
- FAD, EQ8
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 425 | 30% helix, 25% strand | P9WJF0 |
| B | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 412 | 30% helix, 27% strand | P9WJF0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- EQ8 · [2-(4-cyclohexylsulfonylpiperazin-1-yl)-4-oxidanylidene-6-(trifluoromethyl)-1,3-benzothiazin-8-yl]-oxidanylidene-azanium · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.78 | 0.86 | 63 | FAD, EQ8 |
| 2 | 579 | 0.78 | 0.84 | 76 | FAD, EQ8 |
| 3 | 516 | 0.61 | 0.74 | 58 | empty |
| 4 | 92 | 0.46 | 0.80 | 21 | empty |
| 5 | 118 | 0.36 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6G83 · Crystal structure of M. tuberculosis DprE1 in complex with sPBTZ169 (sulfonylPBTZ) · the same entry in another collection · chain A against A, TM-score 1.00
- P9WJF0 · AlphaFold monomer V2.0 prediction for decaprenylphosphoryl-beta-D- ribose oxidase (P9WJF0) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P9WJF0
- Elsewhere: RCSB PDB 6G83 · PDBe 6G83 · UniProt P9WJF0
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