MolNFT v1 · #129250 · protein
Mycobacterium tuberculosis DPRE1 in complex with inhibitor TCA481
5OEP · Decaprenylphosphoryl-beta-D-ribose oxidase: “Mycobacterium tuberculosis DPRE1 in complex with inhibitor TCA481”. X-ray diffraction, 2 ligands (FAD, 9T2), 4 pockets (best druggability 0.80). MolNFT v1 #129250 on GenesisL1: 3D…
- PDB
- 5OEP
- Type
- protein
- Length
- 842 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
- P9WJF1
- Ligands
- FAD, 9T2
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 426 | 31% helix, 26% strand | P9WJF1 |
| B | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 416 | 31% helix, 27% strand | P9WJF1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 9T2 · ethyl ~{N}-[2-(1,3-benzothiazol-2-ylcarbonylamino)-5-fluoranyl-thiophen-3-yl]carbonylcarbamate · 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 | 492 | 0.80 | 0.87 | 54 | FAD, 9T2 |
| 2 | 521 | 0.78 | 0.85 | 64 | FAD, 9T2 |
| 3 | 523 | 0.61 | 0.74 | 46 | empty |
| 4 | 141 | 0.39 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 468 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5OEP · Mycobacterium tuberculosis DprE1 in complex with inhibitor TCA481 · the same entry in another collection · chain A against A, TM-score 1.00
- P9WJF1 · AlphaFold monomer V2.0 prediction for decaprenylphosphoryl-beta-D- ribose oxidase (P9WJF1) · 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 P9WJF1
- Elsewhere: RCSB PDB 5OEP · PDBe 5OEP · UniProt P9WJF1
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