4KNZ

Thymidylate synthase ternary complex with dUMP AND CB3717

Structural Biology Knowledgebase: 4KNZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.154
  • R-Value Work: 0.131

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KNZ

Classification: TRANSFERASE

Total Structure Weight: 62718.14

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidylate synthase A, B 264 Escherichia coli EC#: 2.1.1.45 IUBMB
Gene Name(s): thyA b2827 JW2795

Small Molecules
Ligands 3 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMC
Query on UMC

A, B 2'-deoxy-5'-uridylic acid
C9 H15 N2 O8 P
WQQZADPPRABIFU-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UMC N/A in BindingDB
N/A in BindingMoad
Kd: 8500 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: 1.3 Å
  • R-Value Free: 0.154
  • R-Value Work: 0.131
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 125.41 α = 90.00
b = 125.41 β = 90.00
c = 66.58 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-10
  • Released Date: 2013-05-22
  • Deposition author(s): Newby, Z., Lee, T.T., Finer-Moore, J., Stroud, R.M.
  • Previous versions: 2G8O 4IW5

Revision History

  • 2013-06-05
    Type: Citation | Details: Citation update