6K79 | pdb_00006k79

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
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: 2.19 Å
R-Value Free:
0.238 (Depositor), 0.241 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6K79

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: 16,106
Modeled Residue Count: 1,961
Deposited Residue Count: 1,988
Unique protein chains: 2

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O93623
Sequence Annotations Expand
Reference Sequence

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O93623
Sequence Annotations Expand
Reference Sequence

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 B] SDF format, chain G [auth C] SDF format, chain I [auth D] SDF format, chain K [auth A] MOL2 format, chain E [auth B] MOL2 format, chain G [auth C] MOL2 format, chain I [auth D] MOL2 format, chain K [auth A] mmCIF format, chain E [auth B] mmCIF format, chain G [auth C] mmCIF format, chain I [auth D] mmCIF format, chain K [auth A]	E [auth B], G [auth C], I [auth D], K [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth C] Focus chain I [auth D] Focus chain K [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth C] Focus chain I [auth D] Focus chain K [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth C] SDF format, chain J [auth D] SDF format, chain L [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] MOL2 format, chain L [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D] mmCIF format, chain L [auth A]	F [auth B], H [auth C], J [auth D], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth A] Interactions & Density Focus chain F [auth B] Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.238 (Depositor), 0.241 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

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 Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-10

Deposition Author(s):

Angkawidjaja, C.

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.