MolNFT v1 · #76861 · protein
Crystal structure of dethiobiotin synthetase (biod) from helicobacter pylori complexed with GTP
3QXJ: “Crystal structure of dethiobiotin synthetase (biod) from helicobacter pylori complexed with GTP”. X-ray diffraction, 3 ligands (GTP, MG, NO3), 2 pockets (best druggability 0.39). MolNFT v1 #76861 on GenesisL1: 3D structure, binding…
- PDB
- 3QXJ
- 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
- GTP, MG, NO3
- Pockets
- 2 · best druggability 0.39
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
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NO3 · Nitrate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · 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 | 108 | 0.39 | 0.75 | 24 | GTP, MG, EDO |
| 2 | 66 | 0.29 | 0.74 | 18 | EDO |
Compared structures
- 3QXJ · 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 3QXJ · PDBe 3QXJ · UniProt O24872
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