4DB3

1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus.

Minasov, G.Wawrzak, Z.Onopriyenko, O.Skarina, T.Papazisi, L.Savchenko, A.Anderson, W.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetyl-D-glucosamine kinaseA327Vibrio vulnificusMutation(s): 0 
Gene Names: nagKVV1_2570
EC: 2.7.1.59
Find proteins for Q8D9M7 (Vibrio vulnificus (strain CMCP6))
Explore Q8D9M7 
Go to UniProtKB:  Q8D9M7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 64
  • Diffraction Data DOI: 10.18430/M34DB3 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.4α = 90
b = 80.4β = 90
c = 110.418γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description