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Crystal structure of dethiobiotin synthetase (biod) from helicobacter pylori complexed with GDP and 8-aminocaprylic acid
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
- 3QXX
- Type
- protein
- Length
- 224 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dethiobiotin synthetase
- EC
- 6.3.3.3
- UniProt
- O24872
- Ligands
- 8AC, GDP, MG, PO4
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dethiobiotin synthetase (EC 6.3.3.3) | protein | 224 | 43% helix, 16% strand | O24872 |
Ligands and binding sites
- 8AC · 8-aminooctanoic acid · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.37 | 0.75 | 25 | 8AC, MG, PO4 |
| 2 | 50 | 0.25 | 0.73 | 15 | EDO |
Compared structures
- 3QXX · Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed… · the same entry in another collection · chain A against A, 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 0.97
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 3QXX · PDBe 3QXX · UniProt O24872
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