Download MendeleyStructural analysis of hexameric structure of glycerol kinase from Thermococcus kodakaraeinsis KOD1
Hokao, R., Matsumura, H., Katsumi, R., Angkawidjaja, C., Takano, K., Kanaya, S., Koga, Y.To be published.
6K79
Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.
- PDB DOI: https://doi.org/10.2210/pdb6K79/pdb
- Classification: TRANSFERASE
- Organism(s): Thermococcus kodakarensis KOD1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2019-06-06 Released: 2020-06-10
- Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.19 Å
- R-Value Free: 0.238
- R-Value Work: 0.185
- R-Value Observed: 0.187
wwPDB Validation 3D Report Full Report
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 |
| Glycerol kinase | A [auth B] | 497 | Thermococcus kodakarensis KOD1 | Mutation(s): 0 Gene Names: glpK, TK1396 EC: 2.7.1.30 |  |
UniProt | |||||
Find proteins for O93623 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore O93623 Go to UniProtKB: O93623 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O93623 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glycerol kinase | B [auth C], C [auth D], D [auth A] | 497 | Thermococcus kodakarensis KOD1 | Mutation(s): 0 Gene Names: glpK, TK1396 EC: 2.7.1.30 |  |
UniProt | |||||
Find proteins for O93623 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore O93623 Go to UniProtKB: O93623 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O93623 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PGE Query on PGE | E [auth B], G [auth C], I [auth D], K [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | F [auth B], H [auth C], J [auth D], L [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.19 Å
- R-Value Free: 0.238
- R-Value Work: 0.185
- R-Value Observed: 0.187
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.041 | α = 103.43 |
| b = 72.128 | β = 94.96 |
| c = 115.994 | γ = 99.48 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-06-10 Deposition Author(s): Koga, Y., Angkawidjaja, C., Matsumura, H., Hokao, R.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Ministry of Education, Culture, Sports, Science and Technology (Japan) | Japan | JP22780091 |
Revision History (Full details and data files)
- Version 1.0: 2020-06-10
Type: Initial release - Version 1.1: 2024-03-27
Changes: Data collection, Database references
