3N3Y

Crystal structure of Thymidylate Synthase X (ThyX) from Helicobacter pylori with FAD and dUMP at 2.31A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.307 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure, Enzymatic Characterization and Inhibitor Discovery of Thymidylate Synthase X (ThyX) from Helicobacter pylori Strain SS1

Wang, K.Wang, Q.Chen, J.Chen, L.Jiang, H.Shen, X.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase thyX
A, B, C, D
216Helicobacter pyloriMutation(s): 0 
Gene Names: thyX
EC: 2.1.1.148
Find proteins for Q5UVJ4 (Helicobacter pylori)
Go to UniProtKB:  Q5UVJ4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.307 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.525α = 90.00
b = 79.956β = 103.14
c = 96.405γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description