3VW3

Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct

Structural Biology Knowledgebase: 3VW3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.247

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VW3

Classification: IMMUNE SYSTEM / DNA

Total Structure Weight: 58903.88


Macromolecule Entities
Molecule Chains Length Organism Details
Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain) L 217 Mus musculus
Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain) H 220 Mus musculus
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3') A 18 synthetic
DNA (5'-D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3') B 18 synthetic

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

H COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
64T
Query on 64T
A DNA LINKING C10 H17 N2 O9 P DT
5PY
Query on 5PY
A DNA LINKING C10 H15 N2 O7 P DT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.247
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.43 α = 90.00
b = 68.43 β = 90.00
c = 243.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-30
  • Released Date: 2013-03-27
  • Deposition author(s): Yokoyama, H., Mizutani, R., Satow, Y.

Revision History

  • 2014-04-30
    Type: Citation | Details: Citation update