Research workbench
Mycobacterium tuberculosis DPRE1 in complex with CT325 - monoclinic crystal form
Analyse Mycobacterium tuberculosis DPRE1 in complex with CT325 - monoclinic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FF6
- Type
- protein
- Length
- 837 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, 0T4
- 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 | 423 | 30% helix, 26% strand | P72056 |
| B | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 414 | 29% helix, 26% strand | P72056 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 0T4 · 3-(hydroxyamino)-N-[(1R)-1-phenylethyl]-5-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 3 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 | 685 | 0.80 | 0.85 | 75 | FAD, 0T4 |
| 2 | 583 | 0.78 | 0.84 | 62 | FAD, 0T4 |
| 3 | 488 | 0.59 | 0.74 | 42 | empty |
| 4 | 133 | 0.40 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 451 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4FF6 · Mycobacterium tuberculosis DprE1 in complex with CT325 - monoclinic crystal form · the same entry in another collection · chain A against A, 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 4FF6 · PDBe 4FF6 · UniProt P72056
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