Research workbench
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase complexed with 7-keto 8-aminopelargonic acid
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
- 3FMI
- Type
- protein
- Length
- 906 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
- KAP, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 231 | 43% helix, 24% strand | O06620 |
| B, D | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 224 | 43% helix, 26% strand | O06620 |
| C | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 227 | 41% helix, 22% strand | O06620 |
Ligands and binding sites
- KAP · 7-keto-8-aminopelargonic acid · ligand · 3 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.83 | 0.84 | 144 | KAP, SO4 |
| 2 | 313 | 0.67 | 0.82 | 53 | SO4 |
| 3 | 289 | 0.64 | 0.81 | 49 | SO4, KAP |
| 4 | 122 | 0.40 | 0.75 | 22 | empty |
| 5 | 128 | 0.38 | 0.74 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1209 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1116 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 125 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 3FMI · Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with… · the same entry in another collection · chain B against B, 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 3FMI · PDBe 3FMI · UniProt O06620
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