Download MendeleyCrystal structure of nucleoside diphosphate kinase in complex with GDP
Kato-Murayama, M., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S.To be published.
2DXE
Crystal structure of nucleoside diphosphate kinase in complex with GDP
- PDB DOI: https://doi.org/10.2210/pdb2DXE/pdb
- Classification: TRANSFERASE
- Organism(s): Pyrococcus horikoshii OT3
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-08-25 Released: 2007-02-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.190
- R-Value Work: 0.168
- R-Value Observed: 0.168
This is version 1.2 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 | A, B | 160 | Pyrococcus horikoshii OT3 | Mutation(s): 0 Gene Names: ndk, PH0698 EC: 2.7.4.6 |  |
UniProt | |||||
Find proteins for O58429 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58429 Go to UniProtKB: O58429 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O58429 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GDP Query on GDP | F [auth A] | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N |  | Ligand Interaction | |
| CL Query on CL | D [auth A], E [auth A], G [auth B], H [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| MG Query on MG | C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.190
- R-Value Work: 0.168
- R-Value Observed: 0.168
- Space Group: P 63
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 69.802 | α = 90 |
| b = 69.802 | β = 90 |
| c = 107.093 | γ = 120 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| CrystalClear | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-02-25 Deposition Author(s): Kato-Murayama, M., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2007-02-25
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
