2QM1 | pdb_00002qm1

Crystal structure of glucokinase from Enterococcus faecalis

PDB DOI: https://doi.org/10.2210/pdb2QM1/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-07-13 Released: 2007-07-31
Deposition Author(s): Kim, Y., Joachimiak, G., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.230 (Depositor), 0.227 (DCC)
R-Value Work:
0.186 (Depositor), 0.183 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Glucokinase from Enterococcus faecalis.

Kim, Y., Joachimiak, G., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 140.14 kDa
Atom Count: 11,092
Modeled Residue Count: 1,297
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A, B, C, D	326	Enterococcus faecalis V583	Mutation(s): 4 Gene Names: glcK, EF_2788 EC: 2.7.1.2
UniProt
Find proteins for Q830J4 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830J4 Go to UniProtKB: Q830J4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q830J4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D]	T [auth D], U [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain T [auth D] Focus chain U [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] L [auth B] P [auth C] G [auth A], H [auth A], I [auth A], L [auth B], P [auth C], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], M [auth C], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], N [auth C], O [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.230 (Depositor), 0.227 (DCC)
R-Value Work: 0.186 (Depositor), 0.183 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.083	α = 90
b = 131.26	β = 92.48
c = 82.763	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
autoSHARP	phasing
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-07-31

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-07-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary