Download MendeleyCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-637
Singh, A.K., Brown, D.G.To be published.
6FRD
Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-637
- PDB DOI: https://doi.org/10.2210/pdb6FRD/pdb
- Classification: HYDROLASE
- Organism(s): Trypanosoma brucei
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-02-15 Released: 2019-03-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.209
- R-Value Work: 0.169
- R-Value Observed: 0.171
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 | |
| E3Q Query on E3Q | P [auth B] | 1-cycloheptyl-3-{4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl}-4,4-dimethyl-4,5-dihydro- 1H-pyrazol-5-one C27 H34 N2 O4 KQFIOHKLWWEPIB-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | C [auth A], K [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| GAI Query on GAI | E [auth A] F [auth A] G [auth A] J [auth A] M [auth B] | GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N |  | ||
| FMT Query on FMT | H [auth A], I [auth A] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A], L [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.209
- R-Value Work: 0.169
- R-Value Observed: 0.171
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 113.98 | α = 90 |
| b = 113.48 | β = 107.89 |
| c = 68.22 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2019-03-13 Deposition Author(s): Singh, A.K., Brown, D.G.
Revision History (Full details and data files)
- Version 1.0: 2019-03-13
Type: Initial release - Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
