4LRR

Ternary complex between E. coli thymidylate synthase, dUMP, and F9

Structural Biology Knowledgebase: 4LRR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.170

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4LRR

Classification: TRANSFERASE

Total Structure Weight: 31999.94

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidylate synthase A 265 Escherichia coli EC#: 2.1.1.45 IUBMB
Gene Name(s): thyA Z4144 ECs3684
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CF9
Query on CF9

A 2-oxo-2H-naphtho[1,8-bc]furan-6-yl 4-nitrobenzoate
C18 H9 N O6
JZRRRFGHBXIXDI-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMP
Query on UMP

A 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP (Synonym)
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CF9 N/A in BindingDB
Ki: 6000 nM  BindingMOAD
Ki: 6000 nM  PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
A NON-POLYMER C2 H4 O --
SCH
Query on SCH
A L-PEPTIDE LINKING C4 H9 N O2 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.170
  • Space Group: I 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 131.18 α = 90.00
b = 131.18 β = 90.00
c = 131.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-07-20
  • Released Date: 2013-11-06
  • Deposition author(s): Mangani, S., Pozzi, C., Ferrari, S., Costi, M.P.

Revision History

  • 2013-12-11
    Type: Citation | Details: Citation update