Download MendeleyTbrPDEB1 structure with inhibitor NPD-356
Salado, I.G., Moreno, C., Sakaine, G., Singh, A.K., Blaazer, A.R., Siderius, M., Matheeussen, A., Gul, S., Maes, L., Leurs, R., Brown, D.G., Augustyns, K.To be published.
6FDW
Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-356
- PDB DOI: https://doi.org/10.2210/pdb6FDW/pdb
- Classification: HYDROLASE
- Organism(s): Trypanosoma brucei
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-12-27 Released: 2019-04-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.96 Å
- R-Value Free: 0.237
- R-Value Work: 0.190
- R-Value Observed: 0.192
Starting Model: experimental
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This is version 1.1 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 |
| Phosphodiesterase | 360 | Trypanosoma brucei | Mutation(s): 0 Gene Names: PDEB1 EC: 3.1.4 |  | |
UniProt | |||||
Find proteins for Q8WQX9 (Trypanosoma brucei) Explore Q8WQX9 Go to UniProtKB: Q8WQX9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8WQX9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| D62 Query on D62 | C [auth A], H [auth B] | (4aS,8aR)-2-(1-{2-aminothieno[2,3-d]pyrimidin-4-yl}piperidin-4-yl)-4-(3,4- dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one C27 H30 N6 O3 S VRSCGUCAJHMOSB-RBUKOAKNSA-N |  | ||
| GOL Query on GOL | G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | D [auth A], I [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| GAI Query on GAI | F [auth A] | GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N |  | ||
| MG Query on MG | E [auth A], J [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.96 Å
- R-Value Free: 0.237
- R-Value Work: 0.190
- R-Value Observed: 0.192
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 111.69 | α = 90 |
| b = 119.26 | β = 108.38 |
| c = 67.97 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2019-04-10 Deposition Author(s): Singh, A.K., Brown, D.G.
Revision History (Full details and data files)
- Version 1.0: 2019-04-10
Type: Initial release - Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
