1NCE

Crystal structure of a ternary complex of E. coli thymidylate synthase D169C with dUMP and the antifolate CB3717

Structural Biology Knowledgebase: 1NCE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 1NCE

Classification: BIOSYNTHETIC PROTEIN

Total Structure Weight: 62667.23

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidylate synthase A, B 264 Escherichia coli EC#: 2.1.1.45 IUBMB
Mutation: M1X, D169C
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
CB3
Query on CB3

A, B 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
C24 H23 N5 O6
LTKHPMDRMUCUEB-IBGZPJMESA-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 %)
CB3 IC50: 19 - 5800 nM (99) BindingDB
Ki: 60 nM (99) BindingDB

N/A in BindingMoad
N/A in 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: 2.4 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.187
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 127.10 α = 90.00
b = 127.10 β = 90.00
c = 68.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-05
  • Released Date: 2002-12-25
  • Deposition author(s): Birdsall, D.L., Finer-Moore, J., Stroud, R.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update