2ONB

Human Thymidylate Synthase at low salt conditions with PDPA bound

Structural Biology Knowledgebase: 2ONB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ONB

Classification: TRANSFERASE

Total Structure Weight: 36429.88

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidylate synthetase A 313 Homo sapiens EC#: 2.1.1.45 IUBMB
Mutation: C43X, C180X, C195X, C199X
Gene Name(s): TYMS Gene View TS OK/SW-cl.29

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
7PA
Query on 7PA

A PROPANE-1,3-DIYLBIS(PHOSPHONIC ACID)
C3 H10 O6 P2
PUVMVPFLXCHEOY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
7PA Ki: 260 - 2700 nM (100) BindingDB

N/A in BindingMoad
Ki: 2700 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.216
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 95.69 α = 90.00
b = 95.69 β = 90.00
c = 82.50 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-01-23
  • Released Date: 2007-04-10
  • Deposition author(s): Lovelace, L.L., Gibson, L.M., Lebioda, L.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4