MolNFT v1 · #151153 · protein
M tuberculosis DPRE1 in complex with a covalently bound nitrobenzothiazinone
6HF3 · Decaprenylphosphoryl-beta-D-ribose oxidase: “M tuberculosis DPRE1 in complex with a covalently bound nitrobenzothiazinone”. X-ray diffraction, 2 ligands (26J, FAD), 4 pockets (best druggability 0.80). MolNFT v1 #151153 on GenesisL1…
- PDB
- 6HF3
- Type
- protein
- Length
- 841 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
- 26J, FAD
- 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 | 427 | 30% helix, 25% strand | P9WJF1 |
| B | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 414 | 31% helix, 26% strand | P9WJF1 |
Ligands and binding sites
- 26J · 2-(4-(cyclohexylmethyl)piperazin-1-yl)-8-nitro-6-(trifluoromethyl)-4H-benzo[e][1,3]thiazin-4-one, bound form · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · 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 | 828 | 0.80 | 0.83 | 95 | 26J, FAD |
| 2 | 554 | 0.79 | 0.86 | 69 | 26J, FAD |
| 3 | 420 | 0.56 | 0.73 | 42 | empty |
| 4 | 54 | 0.41 | 0.82 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 452 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6HF3 · M tuberculosis DprE1 in complex with a covalently bound nitrobenzothiazi · 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 0.97
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 6HF3 · PDBe 6HF3 · UniProt P9WJF1
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