Download MendeleyCrystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to CDP
Gardberg, A.S., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)To be published.
4FKX
Crystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to CDP
- PDB DOI: https://doi.org/10.2210/pdb4FKX/pdb
- Classification: TRANSFERASE
- Organism(s): Trypanosoma brucei brucei TREU927
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2012-06-13 Released: 2012-06-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.182
- R-Value Work: 0.152
- R-Value Observed: 0.154
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 |
| Nucleoside diphosphate kinase | 161 | Trypanosoma brucei brucei TREU927 | Mutation(s): 0 Gene Names: Tb11.01.7800 EC: 2.7.4.6 |  | |
UniProt | |||||
Find proteins for Q381H3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q381H3 Go to UniProtKB: Q381H3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q381H3 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CDP Query on CDP | D [auth A], F [auth B], I [auth C] | CYTIDINE-5'-DIPHOSPHATE C9 H15 N3 O11 P2 ZWIADYZPOWUWEW-XVFCMESISA-N |  | ||
| MPD Query on MPD | H [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| MG Query on MG | E [auth A], G [auth B], J [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.182
- R-Value Work: 0.152
- R-Value Observed: 0.154
- Space Group: C 2 2 21
- Diffraction Data: https://doi.org/10.18430/M34FKX
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 71.63 | α = 90 |
| b = 121.37 | β = 90 |
| c = 112.87 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| StructureStudio | data collection |
Entry History
Deposition Data
- Released Date: 2012-06-27 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2012-06-27
Type: Initial release - Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
