MolNFT v1 · #75709 · protein
Crystal structure of ent-copalyl diphosphate synthase from arabidopsis thaliana in complex with 13-aza-13,14-dihydrocopalyl diphosphate
3PYB · Ent-copalyl diphosphate synthase, chloroplastic: “Crystal structure of ent-copalyl diphosphate synthase from arabidopsis thaliana in complex with…”. X-ray diffraction, 1 ligand (A3C), 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 3PYB
- Type
- protein
- Length
- 2,059 residues
- Chains
- 3
- 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
- A3C
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ent-copalyl diphosphate synthase, chloroplastic (EC 5.5.1.13) | protein | 685 | 65% helix, 2% strand | Q38802 |
| B | Ent-copalyl diphosphate synthase, chloroplastic (EC 5.5.1.13) | protein | 689 | 66% helix, 3% strand | Q38802 |
Ligands and binding sites
- A3C · 2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen diphosphate · ligand · chains A
- 1PE · Pentaethylene glycol · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.82 | 0.86 | 72 | 1PE |
| 2 | 658 | 0.82 | 0.86 | 70 | 1PE |
| 3 | 632 | 0.81 | 0.86 | 61 | 1PE |
| 4 | 843 | 0.80 | 0.83 | 61 | empty |
| 5 | 792 | 0.80 | 0.83 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 366 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3PYB · 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 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 Q38802
- Elsewhere: RCSB PDB 3PYB · PDBe 3PYB · UniProt Q38802
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