MolNFT v1 · #64474 · protein
Crystal structure of (+)-delta-cadinene synthase from gossypium arboreum and evolutionary divergence of metal binding motifs for catalysis
3G4D · (+)-delta-cadinene synthase isozyme XC1: “Crystal structure of (+)-delta-cadinene synthase from gossypium arboreum and evolutionary divergence of metal…”. X-ray diffraction, 16 pockets (best druggability 0.77). MolNFT v1 #64474 on…
- PDB
- 3G4D
- Type
- protein
- Length
- 1,028 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
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (+)-delta-cadinene synthase isozyme XC1 (EC 4.2.3.13) | protein | 516 | 72% helix, 0% strand | Q39761 |
| B | (+)-delta-cadinene synthase isozyme XC1 (EC 4.2.3.13) | protein | 512 | 70% helix, 0% strand | Q39761 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.77 | 0.87 | 50 | empty |
| 2 | 335 | 0.77 | 0.88 | 48 | GOL |
| 3 | 831 | 0.76 | 0.80 | 88 | empty |
| 4 | 463 | 0.71 | 0.81 | 55 | GOL |
| 5 | 432 | 0.59 | 0.75 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 685 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3G4D · Crystal Structure of (+)-delta-Cadinene Synthase from Gossypium arboreum and Evolutionary… · 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 3G4D · PDBe 3G4D · UniProt Q39761
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