MolNFT v1 · #158483 · protein
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with triazole linked compound 9
6NVD · ATP-dependent dethiobiotin synthetase biod: “Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with triazole linked…”. X-ray diffraction, 2 ligands (L4S, SO4), 10 pockets (best druggability 0.74).…
- PDB
- 6NVD
- Type
- protein
- Length
- 905 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent dethiobiotin synthetase biod
- EC
- 6.3.3.3
- UniProt
- P9WPQ5
- Ligands
- L4S, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 41% helix, 22% strand | P9WPQ5 |
| B, C, D | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 226 | 42% helix, 25% strand | P9WPQ5 |
Ligands and binding sites
- L4S · 2',5'-dideoxy-5'-[4-({[(1S,2R)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetyl}amino)-1H-1,2,3-triazol-1-yl]cytidine · ligand · chains C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.74 | 0.80 | 59 | empty |
| 2 | 253 | 0.70 | 0.86 | 50 | SO4 |
| 3 | 306 | 0.64 | 0.81 | 48 | L4S, SO4 |
| 4 | 266 | 0.64 | 0.82 | 43 | SO4 |
| 5 | 214 | 0.63 | 0.83 | 46 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1150 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1136 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 349 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 170 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NVD · 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 D 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 6NVD · PDBe 6NVD · UniProt P9WPQ5
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