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 | pdb_00006fdw
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 ?
- R-Value Free: 0.237 (Depositor), 0.240 (DCC)
- R-Value Work: 0.190 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.192 (Depositor)
Starting Model: experimental
View more details
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 ?
- R-Value Free: 0.237 (Depositor), 0.240 (DCC)
- R-Value Work: 0.190 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.192 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( ? ) | 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
