Download MendeleyThe crystal structure of G.acetivorans RNA kinase Ark1
Cao, C.L., Gan, J.H.To be published.
8YV5 | pdb_00008yv5
The crystal structure of G. acetivorans RNA kinase Ark1 in complex with ATP
- PDB DOI: https://doi.org/10.2210/pdb8YV5/pdb
- Classification: TRANSFERASE
- Organism(s): Geoglobus acetivorans
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-03-28 Released: 2025-04-02
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 ?
- R-Value Free: 0.216 (Depositor), 0.216 (DCC)
- R-Value Work: 0.178 (Depositor), 0.181 (DCC)
- R-Value Observed: 0.180 (Depositor)
Starting Model: in silico
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This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Putative serine/threonine protein kinase | A [auth B], B [auth A] | 175 | Geoglobus acetivorans | Mutation(s): 0 Gene Names: GACE_0057 |  |
UniProt | |||||
Find proteins for A0A0A7GDU7 (Geoglobus acetivorans) Explore A0A0A7GDU7 Go to UniProtKB: A0A0A7GDU7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0A7GDU7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP (Subject of Investigation/LOI) Query on ATP | D [auth B], G [auth A] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| GOL (Subject of Investigation/LOI) Query on GOL | C [auth B], F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL (Subject of Investigation/LOI) Query on CL | E [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 ?
- R-Value Free: 0.216 (Depositor), 0.216 (DCC)
- R-Value Work: 0.178 (Depositor), 0.181 (DCC)
- R-Value Observed: 0.180 (Depositor)
Space Group: I 21 3
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 146.92 | α = 90 |
| b = 146.92 | β = 90 |
| c = 146.92 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-04-02
Type: Initial release
