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Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with dethiobiotin and phosphate
Analyse Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FPA
- Type
- protein
- Length
- 909 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Mycobacterium tuberculosis
- Molecule
- Dethiobiotin synthetase
- EC
- 6.3.3.3
- UniProt
- O06620
- Ligands
- DTB, MG, PO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.3 · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 230 | 43% helix, 21% strand | O06620 |
| B | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 226 | 42% helix, 24% strand | O06620 |
| C | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 228 | 41% helix, 24% strand | O06620 |
| D | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 225 | 42% helix, 23% strand | O06620 |
Ligands and binding sites
- DTB · 6-(5-methyl-2-oxo-imidazolidin-4-yl)-hexanoic acid · ligand · 3 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 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 | 1141 | 0.79 | 0.80 | 113 | PO4, MG |
| 2 | 427 | 0.71 | 0.82 | 72 | DTB, PO4, MG |
| 3 | 327 | 0.67 | 0.81 | 52 | PO4, MG, DTB |
| 4 | 316 | 0.64 | 0.81 | 55 | DTB, PO4, MG |
| 5 | 104 | 0.35 | 0.74 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1148 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1052 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 383 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 122 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 3FPA · Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
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 O06620
- Elsewhere: RCSB PDB 3FPA · PDBe 3FPA · UniProt O06620
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