1JUT

E. coli Thymidylate Synthase Bound to dUMP and LY338529, A Pyrrolo(2,3-d)pyrimidine-based Antifolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 1JUT

Classification: TRANSFERASE

Total Structure Weight: 62530.55

Macromolecule Entities
Molecule Chains Length Organism Details
THYMIDYLATE SYNTHASE A, B 264 Escherichia coli EC#: 2.1.1.45 IUBMB
Mutation: M1X
Gene Name(s): thyA b2827 JW2795
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LYD
Query on LYD

A, B 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3- D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-3- METHYL-BUTYRIC ACID
LY338529 (Synonym)
C20 H23 N5 O4
MYENGRJSPURSQB-HNNXBMFYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMP
Query on UMP

A, B 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP (Synonym)
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LYD N/A in BindingDB
N/A in BindingMoad
Ki: 47.7 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CXM
Query on CXM
A, B L-PEPTIDE LINKING C6 H11 N O4 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.218
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 125.80 α = 90.00
b = 125.80 β = 90.00
c = 67.06 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-08-27
  • Released Date: 2001-09-19
  • Deposition author(s): Sayre, P.H., Finer-Moore, J.S., Fritz, T.A., Biermann, D., Gates, S.B., MacKellar, W.C., Patel, V.F., Stroud, R.M.

Revision History

  • 2008-04-27
    Type: Version format compliance
  • 2011-07-13
    Type: Non-polymer description, Version format compliance