3IVE

Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Cytidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Cytidine

Ramagopal, U.A.Toro, R.Burley, S.K.Almo, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleotidase
A
509Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Find proteins for A0A0H2VD83 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  A0A0H2VD83
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
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
FE
Query on FE

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Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CTN
Query on CTN

Download SDF File 
Download CCD File 
A
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
CYTIDINE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.261α = 90.00
b = 77.453β = 103.83
c = 47.518γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description