Research workbench
Mycobacterium tuberculosis DPRE1 in complex with inhibitor TCA020
Analyse Mycobacterium tuberculosis DPRE1 in complex with inhibitor TCA020 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OEQ
- Type
- protein
- Length
- 843 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decaprenylphosphoryl-beta-D-ribose oxidase
- UniProt
- I6X8C4
- Ligands
- FAD, P95
- 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 | Decaprenylphosphoryl-beta-D-ribose oxidase | protein | 426 | 30% helix, 26% strand | I6X8C4 |
| B | Decaprenylphosphoryl-beta-D-ribose oxidase | protein | 417 | 31% helix, 26% strand | I6X8C4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- P95 · ~{N}-[3-(pyrimidin-2-ylcarbamoyl)thiophen-2-yl]-[1, 3]thiazolo[4,5-c]pyridine-2-carboxamide · ligand · chains A
- 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 | 621 | 0.80 | 0.85 | 76 | FAD, P95 |
| 2 | 509 | 0.78 | 0.85 | 61 | FAD |
| 3 | 540 | 0.61 | 0.74 | 49 | empty |
| 4 | 105 | 0.34 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 464 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5OEQ · Mycobacterium tuberculosis DprE1 in complex with inhibitor TCA020 · 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 I6X8C4
- Elsewhere: RCSB PDB 5OEQ · PDBe 5OEQ · UniProt I6X8C4
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