6K78

Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.

PDB DOI: https://doi.org/10.2210/pdb6K78/pdb

Classification: TRANSFERASE
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-06 Released: 2020-06-10
Deposition Author(s): Koga, Y., Angkawidjaja, C., Matsumura, H., Hokao, R.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.273 (Depositor), 0.270 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural 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.

Macromolecule Content

Total Structure Weight: 224.86 kDa
Atom Count: 15,211
Modelled Residue Count: 1,865
Deposited Residue Count: 1,988
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol kinase	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 Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol kinase	B, C, D	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 Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]