Download MendeleyStructure of ent-Copalyl Diphosphate Synthase from Arabidopsis thaliana, a Protonation-Dependent Diterpene Cyclase
Koksal, M., Hu, H., Coates, R.M., Peters, R.J., Christianson, D.W.To be published.
3PYA
Crystal structure of ent-copalyl diphosphate synthase from Arabidopsis thaliana in complex with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate
- PDB DOI: https://doi.org/10.2210/pdb3PYA/pdb
- Classification: ISOMERASE
- Organism(s): Arabidopsis thaliana
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-12-12 Released: 2011-05-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.233
- R-Value Work: 0.172
- R-Value Observed: 0.176
Starting Model: experimental
View more details
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ent-copalyl diphosphate synthase, chloroplastic | 727 | Arabidopsis thaliana | Mutation(s): 0 Gene Names: At4g02780, GA1, T5J8.9, TPSGA1 EC: 5.5.1.13 |  | |
UniProt | |||||
Find proteins for Q38802 (Arabidopsis thaliana) Explore Q38802 Go to UniProtKB: Q38802 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q38802 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AG8 Query on AG8 | B [auth A] | S-[(2E,6E,10E)-14-(dimethylamino)-3,7,11-trimethyltetradeca-2,6,10-trien-1-yl] trihydrogen thiodiphosphate C19 H37 N O6 P2 S WNRLOKILDUQQLN-WNWLUAIZSA-N |  | ||
| 1PE Query on 1PE | D [auth A] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | C [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.233
- R-Value Work: 0.172
- R-Value Observed: 0.176
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.316 | α = 90 |
| b = 114.314 | β = 90 |
| c = 129.412 | γ = 90 |
| Software Name | Purpose |
|---|---|
| APS | data collection |
| PHENIX | model building |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
Entry History
Deposition Data
- Released Date: 2011-05-25 Deposition Author(s): Koksal, M., Christianson, D.W.
Revision History (Full details and data files)
- Version 1.0: 2011-05-25
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
