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Crystal structure of 10-epi-cubebol synthase from Sorangium cellulosum (ScCubS) in complex with Pyrophosphate
Analyse Crystal structure of 10-epi-cubebol synthase from Sorangium cellulosum (ScCubS)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZRN
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Sorangium cellulosum
- Molecule
- 10-epi-cubebol synthase
- EC
- 4.2.3.175
- UniProt
- A9GK58
- Ligands
- PPV, MG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.82 · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 10-epi-cubebol synthase (EC 4.2.3.175) | protein | 301 | 75% helix, 0% strand | A9GK58 |
| B | 10-epi-cubebol synthase (EC 4.2.3.175) | protein | 301 | 74% helix, 0% strand | A9GK58 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- ACT · Acetate ion · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.84 | 0.88 | 64 | empty |
| 2 | 174 | 0.81 | 0.96 | 32 | PPV, MG |
| 3 | 299 | 0.79 | 0.90 | 47 | PPV, MG |
| 4 | 101 | 0.58 | 0.86 | 16 | empty |
| 5 | 108 | 0.53 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1292 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- A9GK58 · AlphaFold monomer V2.0 prediction for 10-epi-cubebol synthase (A9GK58) · a predicted model of the same protein · chain B 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 A9GK58
- Elsewhere: RCSB PDB 7ZRN · PDBe 7ZRN · UniProt A9GK58
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