Research workbench
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate
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
- 3FMF
- Type
- protein
- Length
- 908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dethiobiotin synthetase
- EC
- 6.3.3.3
- UniProt
- O06620
- Ligands
- DSD
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 230 | 43% helix, 23% strand | O06620 |
| B | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 228 | 43% helix, 23% strand | O06620 |
| D | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 220 | 43% helix, 23% strand | O06620 |
Ligands and binding sites
- DSD · 7-(carboxyamino)-8-amino-nonanoic acid · ligand · 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 | 1110 | 0.79 | 0.80 | 113 | DSD |
| 2 | 289 | 0.70 | 0.84 | 57 | DSD |
| 3 | 317 | 0.64 | 0.80 | 60 | DSD |
| 4 | 236 | 0.60 | 0.80 | 44 | DSD |
| 5 | 125 | 0.41 | 0.75 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1174 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1155 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 147 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 98 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 3FMF · 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 3FMF · PDBe 3FMF · UniProt O06620
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