Download MendeleyStructure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to ADP
Clifton, M.C., Abendroth, J.A.To be published.
4HR2
Structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to ADP
- PDB DOI: https://doi.org/10.2210/pdb4HR2/pdb
- Classification: TRANSFERASE
- Organism(s): Burkholderia thailandensis E264
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2012-10-26 Released: 2012-11-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.240
- R-Value Work: 0.208
- R-Value Observed: 0.209
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 | 145 | Burkholderia thailandensis E264 | Mutation(s): 0 Gene Names: ndk, BTH_I2231 EC: 2.7.4.6 |  | |
UniProt | |||||
Find proteins for Q2SWE7 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2SWE7 Go to UniProtKB: Q2SWE7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q2SWE7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ADP Query on ADP | C [auth A], D [auth B] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.240
- R-Value Work: 0.208
- R-Value Observed: 0.209
- Space Group: P 41 2 2
- Diffraction Data: https://doi.org/10.18430/M34HR2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 91.24 | α = 90 |
| b = 91.24 | β = 90 |
| c = 90.19 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2012-11-07 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2012-11-07
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
