Download MendeleyTbrPDEB1 structure with inhibitor NPD-226
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.
6FDS
Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-226
- PDB DOI: https://doi.org/10.2210/pdb6FDS/pdb
- Classification: HYDROLASE
- Organism(s): Trypanosoma brucei
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-12-26 Released: 2019-04-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.240
- R-Value Work: 0.193
- R-Value Observed: 0.195
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 | |
| D5T Query on D5T | D [auth A], O [auth B] | 1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi
din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione C30 H38 N4 O6 DZMHUZHTZIODAZ-FCHUYYIVSA-N |  | ||
| GOL Query on GOL | L [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | G [auth A], K [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| GAI Query on GAI | C [auth A] E [auth A] F [auth A] I [auth A] M [auth B] | GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N |  | ||
| MG Query on MG | H [auth A], J [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.240
- R-Value Work: 0.193
- R-Value Observed: 0.195
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 112.72 | α = 90 |
| b = 120.17 | β = 108.05 |
| c = 68.17 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | 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, Structure summary
