3B9H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Studies of Early Events in the Thymidylate Synthase Reaction

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthaseA264Escherichia coliMutation(s): 0 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Explore P0A884 
Go to UniProtKB:  P0A884
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDU
Query on NDU

Download Ideal Coordinates CCD File 
D [auth A]2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE
C9 H14 N3 O10 P
ZYBJIJYGXJSDTC-XZBKPIIZSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
AL-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.6α = 90
b = 71.6β = 90
c = 115.32γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MADNESSdata collection
PROCORdata reduction
PROCORdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2018-04-18
    Changes: Data collection