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Crystal structure of (+)- -cadinene synthase from gossypium arboreum in complex with 2-fluorofarnesyl diphosphate
Analyse Crystal structure of (+)- -cadinene synthase from gossypium arboreum in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G4F
- Type
- protein
- Length
- 1,030 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (+)-delta-cadinene synthase isozyme XC1
- EC
- 4.2.3.13
- UniProt
- Q39761
- Ligands
- FPF, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | (+)-delta-cadinene synthase isozyme XC1 (EC 4.2.3.13) | protein | 515 | 71% helix, 0% strand | Q39761 |
Ligands and binding sites
- FPF · (2Z,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.78 | 0.88 | 57 | empty |
| 2 | 396 | 0.77 | 0.87 | 52 | empty |
| 3 | 724 | 0.77 | 0.81 | 77 | FPF, MG |
| 4 | 525 | 0.76 | 0.83 | 47 | FPF, MG |
| 5 | 516 | 0.63 | 0.76 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 762 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3G4F · Crystal Structure of (+)- -Cadinene Synthase from Gossypium arboreum in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q39761 · AlphaFold monomer V2.0 prediction for (+)-delta-cadinene synthase isozyme XC1 (Q39761) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q39761
- Elsewhere: RCSB PDB 3G4F · PDBe 3G4F · UniProt Q39761
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