MolNFT v1 · #117131 · protein
Geosmin synthase from streptomyces coelicolor N-terminal domain complexed with three MG2+ ions and alendronic acid
5DZ2 · GERMACRADIENOL/GEOSMIN synthase: “Geosmin synthase from streptomyces coelicolor N-terminal domain complexed with three MG2+ ions and alendronic…”. X-ray diffraction, 2 ligands (212, MG), 8 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 5DZ2
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GERMACRADIENOL/GEOSMIN synthase
- EC
- 4.2.3.22, 4.2.3.75, 4.1.99.16
- UniProt
- Q9X839
- Ligands
- 212, MG
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GERMACRADIENOL/GEOSMIN synthase (EC 4.2.3.22, 4.2.3.75, 4.1.99.16) | protein | 322 | 73% helix, 0% strand | Q9X839 |
Ligands and binding sites
- 212 · Alendronate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.86 | 0.97 | 31 | empty |
| 2 | 282 | 0.85 | 0.96 | 37 | MG, 212 |
| 3 | 265 | 0.84 | 0.96 | 36 | MG, 212 |
| 4 | 71 | 0.59 | 0.89 | 16 | empty |
| 5 | 216 | 0.54 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5DZ2 · Geosmin synthase from Streptomyces coelicolor N-terminal domain complexed with three Mg2+… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X839 · AlphaFold monomer V2.0 prediction for GERMACRADIENOL/GEOSMIN synthase (Q9X839) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9X839
- Elsewhere: RCSB PDB 5DZ2 · PDBe 5DZ2 · UniProt Q9X839
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