MolNFT v1 · #151150 · protein
M. tuberculosis DPRE1 covalently bound to a nitrobenzoxacinone.
6HF0 · Decaprenylphosphoryl-beta-D-ribose oxidase: “M. tuberculosis DPRE1 covalently bound to a nitrobenzoxacinone.”. X-ray diffraction, 2 ligands (FAD, G1H), 5 pockets (best druggability 0.80). MolNFT v1 #151150 on GenesisL1: 3D…
- PDB
- 6HF0
- Type
- protein
- Length
- 839 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, G1H
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 424 | 28% helix, 25% strand | P9WJF1 |
| B | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 415 | 28% helix, 26% strand | P9WJF1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- G1H · 2-[(2~{S},6~{R})-2,6-dimethylpiperidin-1-yl]-8-nitro-6-(trifluoromethyl)-1,3-benzoxazin-4-one · 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 | 582 | 0.80 | 0.86 | 76 | FAD, G1H |
| 2 | 566 | 0.80 | 0.86 | 73 | FAD, G1H |
| 3 | 368 | 0.53 | 0.73 | 40 | empty |
| 4 | 143 | 0.39 | 0.73 | 21 | empty |
| 5 | 61 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 443 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6HF0 · M. tuberculosis DprE1 covalently bound to a nitrobenzoxaci . · 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 6HF0 · PDBe 6HF0 · UniProt P9WJF1
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