4FNC

Human TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU)

Structural Biology Knowledgebase: 4FNC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.224

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FNC

Classification: HYDROLASE / DNA

Total Structure Weight: 40637.24


Macromolecule Entities
Molecule Chains Length Organism Details
G/T mismatch-specific thymine DNA glycosylase A 204 Homo sapiens EC#: 3.2.2.29 IUBMB
Fragment: human TDG glycosylase domain, UNP residues 111-308
Gene Name(s): TDG Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (28-MER) C 28 synthetic
DNA (29-MER) D 29 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HMU
Query on HMU

A 5-HYDROXYMETHYL URACIL
5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE (Synonym)
C5 H6 N2 O3
JDBGXEHEIRGOBU-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
AAB
Query on AAB
D DNA LINKING C5 H11 O7 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.224
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 90.96 α = 90.00
b = 53.72 β = 96.49
c = 81.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-06-19
  • Released Date: 2012-09-19
  • Deposition author(s): Hashimoto, H., Hong, S., Bhagwat, A.S., Zhang, X., Cheng, X.

Revision History

  • 2014-07-09
    Type: Non-polymer description | Details: --
  • 2012-11-21
    Type: Citation | Details: Citation update
  • 2012-10-17
    Type: Citation | Details: Citation update