Research workbench
Mycobacterium tuberculosis DPRE1 in complex with CMP2
Analyse Mycobacterium tuberculosis DPRE1 in complex with CMP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HFV
- 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
- EC
- 1.1.98.3
- UniProt
- P9WJF1
- Ligands
- FAD, G1T
- Pockets
- 6 · best druggability 0.82
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, 26% strand | P9WJF1 |
| B | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 416 | 32% helix, 26% strand | P9WJF1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- G1T · 8-(oxidanylamino)-2-piperidin-1-yl-6-(trifluoromethyl)-1,3-benzothiazin-4-one · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.82 | 0.86 | 73 | FAD, G1T, IMD |
| 2 | 887 | 0.81 | 0.83 | 96 | FAD, G1T |
| 3 | 512 | 0.61 | 0.75 | 46 | empty |
| 4 | 59 | 0.45 | 0.83 | 22 | empty |
| 5 | 74 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 477 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6HFV · Mycobacterium tuberculosis DprE1 in complex with CMP2 · 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 6HFV · PDBe 6HFV · UniProt P9WJF1
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