Research workbench
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 8
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
- 6NVF
- Type
- protein
- Length
- 909 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
- L5A, L5J, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 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 | 43% helix, 25% strand | P9WPQ5 |
| B | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 226 | 43% helix, 25% strand | P9WPQ5 |
| C | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 229 | 43% helix, 24% strand | P9WPQ5 |
| D | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 43% helix, 23% strand | P9WPQ5 |
Ligands and binding sites
- L5A · (4-{[(1S,2S)-2-(carboxymethyl) cyclopentyl]methyl}phenyl)acetic acid · ligand · 4 copies · chains A, B, C, D
- L5J · (4-{[(1R,2R)-2-(carboxymethyl) cyclopentyl]methyl}phenyl)acetic acid · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.79 | 0.81 | 106 | L5J, L5A, SO4 |
| 2 | 289 | 0.67 | 0.83 | 47 | L5A, SO4 |
| 3 | 307 | 0.66 | 0.81 | 51 | L5A, L5J, SO4 |
| 4 | 303 | 0.65 | 0.81 | 48 | L5A, SO4 |
| 5 | 123 | 0.40 | 0.76 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1129 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1089 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 126 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6NVF · 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 6NVF · PDBe 6NVF · UniProt P9WPQ5
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