Research workbench
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine triphosphate (ATP) - promiscuous binding mode with disordered nucleoside
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
- 6CVV
- Type
- protein
- Length
- 908 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
- ATP, MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 43% helix, 26% strand | P9WPQ5 |
| B | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 226 | 42% helix, 26% strand | P9WPQ5 |
| C | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 228 | 39% helix, 24% strand | P9WPQ5 |
| D | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 40% helix, 23% strand | P9WPQ5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.75 | 0.78 | 69 | empty |
| 2 | 310 | 0.62 | 0.79 | 47 | ATP, MG |
| 3 | 292 | 0.62 | 0.80 | 50 | ATP |
| 4 | 233 | 0.61 | 0.81 | 47 | ATP |
| 5 | 276 | 0.61 | 0.80 | 45 | ATP, MG |
Interfaces
4 interfaces between chains.
- A–B · 1208 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1098 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 248 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 118 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6CVV · 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 A 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 6CVV · PDBe 6CVV · UniProt P9WPQ5
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