Research workbench
Crystal structure of dethiobiotin synthetase (biod) from helicobacter pylori cocrystallized with ATP
Analyse Crystal structure of dethiobiotin synthetase (biod) from helicobacter pylori… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MLE
- Type
- protein
- Length
- 1,335 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dethiobiotin synthetase
- EC
- 6.3.3.3
- UniProt
- O24872
- Ligands
- 8AC, ADP, MG, PO4, NO3, CL
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 221 | 42% helix, 19% strand | O24872 |
| B | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 224 | 42% helix, 17% strand | O24872 |
| C, D, F | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 223 | 42% helix, 17% strand | O24872 |
Ligands and binding sites
- 8AC · 8-aminooctanoic acid · ligand · 6 copies · chains A, C, B, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, E, D, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F
- NO3 · Nitrate ion · ion · 3 copies · chains A, B, F
- CL · Chloride ion · ion · 3 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.75 | 0.78 | 137 | 8AC, PO4, MG, ADP |
| 2 | 286 | 0.63 | 0.80 | 40 | PO4, MG, ADP, 8AC |
| 3 | 235 | 0.60 | 0.80 | 43 | PO4, MG, ADP, 8AC |
| 4 | 183 | 0.60 | 0.82 | 32 | 8AC, PO4, MG |
| 5 | 172 | 0.59 | 0.82 | 33 | 8AC, PO4, MG |
Interfaces
5 interfaces between chains.
- B–D · 1439 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1429 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1371 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 735 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 676 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3MLE · Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori… · the same entry in another collection · chain F against F, TM-score 1.00
- O24872 · AlphaFold monomer V2.0 prediction for ATP-dependent dethiobiotin synthetase biod (O24872) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O24872
- Elsewhere: RCSB PDB 3MLE · PDBe 3MLE · UniProt O24872
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