Research workbench
Crystal structure of ent-copalyl diphosphate synthase from arabidopsis thaliana in complex with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate at 1.55 a resolution
Analyse Crystal structure of ent-copalyl diphosphate synthase from arabidopsis thaliana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LIX
- Type
- protein
- Length
- 678 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ent-copalyl diphosphate synthase, chloroplastic
- EC
- 5.5.1.13
- UniProt
- Q38802
- Ligands
- AG8, PO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ent-copalyl diphosphate synthase, chloroplastic (EC 5.5.1.13) | protein | 678 | 66% helix, 2% strand | Q38802 |
Ligands and binding sites
- AG8 · S-[(2E,6E,10E)-14-(dimethylamino)-3,7,11-trimethyltetradeca-2,6,10-trien-1-yl] trihydrogen thiodiphosphate · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.80 | 0.83 | 55 | empty |
| 2 | 530 | 0.78 | 0.84 | 58 | AG8 |
| 3 | 298 | 0.59 | 0.77 | 29 | empty |
| 4 | 206 | 0.52 | 0.77 | 28 | empty |
| 5 | 105 | 0.42 | 0.77 | 18 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4LIX · Crystal structure of ent-copalyl diphosphate synthase from Arabidopsis thaliana in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q38802 · AlphaFold monomer V2.0 prediction for ent-copalyl diphosphate synthase, chloroplastic… · a predicted model of the same protein · chain A 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 Q38802
- Elsewhere: RCSB PDB 4LIX · PDBe 4LIX · UniProt Q38802
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