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 

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetyl-D-glucosamine kinase
A
327Vibrio vulnificus (strain CMCP6)Mutation(s): 0 
Gene Names: nagK
EC: 2.7.1.59
Find proteins for Q8D9M7 (Vibrio vulnificus (strain CMCP6))
Go to UniProtKB:  Q8D9M7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 80.400α = 90.00
b = 80.400β = 90.00
c = 110.418γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
Blu-Icedata collection
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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