1DDU

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2',5'-DIDEOXYURIDINE (DDURD)

Structural Biology Knowledgebase: 1DDU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 1DDU

Classification: METHYLTRANSFERASE

Total Structure Weight: 62657.12

Macromolecule Entities
Molecule Chains Length Organism Details
THYMIDYLATE SYNTHASE A, B 265 Escherichia coli EC#: 2.1.1.45 IUBMB
Gene Name(s): thyA b2827 JW2795
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DDU
Query on DDU

A, B 2'-5'DIDEOXYURIDINE
C9 H12 N2 O4
FDCFKLBIAIKUKB-GKROBHDKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CB3 IC50: 19 - 72 nM (100) BindingDB
Ki: 60 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FMT
Query on FMT
A, B NON-POLYMER C H2 O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.188
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 127.40 α = 90.00
b = 127.40 β = 90.00
c = 68.20 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-06-26
  • Released Date: 1998-07-01
  • Deposition author(s): Stout, T.J., Sage, C.R., Stroud, R.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4