3BFI

E. Coli Thymidylate Synthase Y209M mutant complexed with 5-nitro-dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

E.Coli thymidylate synthase complexed with 5-NITRO-2'-DEOXY URIDINE

Arendall, W.B.Hyatt, D.C.Roberts, S.A.Dahlgran, A.L.Maley, F.Montfort, W.R.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A
264Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A884
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE
C9 H14 N3 O10 P
ZYBJIJYGXJSDTC-XZBKPIIZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A
L-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 133.020α = 90.00
b = 133.020β = 90.00
c = 133.020γ = 90.00
Software Package:
Software NamePurpose
PROCORdata scaling
REFMACrefinement
PROCORdata reduction
MADNESSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2018-04-18
    Type: Data collection