Research workbench
Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 3a
Analyse Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NWG
- Type
- protein
- Length
- 908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.939
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- ATP-dependent dethiobiotin synthetase BioD
- EC
- 6.3.3.3
- UniProt
- P9WPQ5
- Ligands
- L6J
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.939 · 4 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent dethiobiotin synthetase BioD (EC 6.3.3.3) | protein | 227 | 44% helix, 25% strand | P9WPQ5 |
| B | ATP-dependent dethiobiotin synthetase BioD (EC 6.3.3.3) | protein | 226 | 43% helix, 27% strand | P9WPQ5 |
| C | ATP-dependent dethiobiotin synthetase BioD (EC 6.3.3.3) | protein | 228 | 42% helix, 22% strand | P9WPQ5 |
| D | ATP-dependent dethiobiotin synthetase BioD (EC 6.3.3.3) | protein | 227 | 44% helix, 22% strand | P9WPQ5 |
Ligands and binding sites
- L6J · [(1R,2R)-2-(2-methoxybenzene-1-carbonyl) cyclopentyl]propanedioic acid · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.71 | 0.81 | 78 | L6J |
| 2 | 810 | 0.71 | 0.77 | 64 | empty |
| 3 | 331 | 0.66 | 0.81 | 51 | empty |
| 4 | 294 | 0.64 | 0.81 | 52 | L6J |
| 5 | 333 | 0.64 | 0.80 | 59 | L6J |
Interfaces
4 interfaces between chains.
- A–B · 1120 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1084 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 285 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 123 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6NWG · Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WPQ5 · AlphaFold monomer V2.0 prediction for dethiobiotin synthetase biod (P9WPQ5) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P9WPQ5
- Elsewhere: RCSB PDB 6NWG · PDBe 6NWG · UniProt P9WPQ5
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