1PW5

putative nagD protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report



Literature

putative nagD protein

Cuff, M.E.Skarina, T.Savchenko, A.Edwards, A.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
nagD protein, putativeA253Thermotoga maritimaMutation(s): 7 
Gene Names: TM1742
Find proteins for Q9X264 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9X264 
Go to UniProtKB:  Q9X264
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download CCD File 
A
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.244 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.788α = 90
b = 97.788β = 90
c = 159.27γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary