1WYW

Crystal Structure of SUMO1-conjugated thymine DNA glycosylase

Structural Biology Knowledgebase: 1WYW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1WYW

Classification: HYDROLASE

Total Structure Weight: 37577.67

Macromolecule Entities
Molecule Chains Length Organism Details
G/T mismatch-specific thymine DNA glycosylase A 230 Homo sapiens EC#: 3.2.2.29 IUBMB
Fragment: central region
Gene Name(s): TDG Gene View
Ubiquitin-like protein SMT3C B 97 Homo sapiens Gene Name(s): SUMO1 Gene View SMT3C SMT3H3 UBL1 OK/SW-cl.43

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

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.205
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.21 α = 90.00
b = 70.42 β = 90.00
c = 106.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-17
  • Released Date: 2005-06-21
  • Deposition author(s): Baba, D., Maita, N., Jee, J.G., Uchimura, Y., Saitoh, H., Sugasawa, K., Hanaoka, F., Tochio, H., Hiroaki, H., Shirakawa, M.

Revision History

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