4A0A

STRUCTURE OF HSDDB1-DRDDB2 BOUND TO A 16 BP CPD-DUPLEX (PYRIMIDINE AT D-1 POSITION) AT 3.6 A RESOLUTION (CPD 3)

Structural Biology Knowledgebase: 4A0A SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.347
  • R-Value Work: 0.263

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4A0A

Classification: DNA BINDING PROTEIN / DNA

Total Structure Weight: 182602.89


Macromolecule Entities
Molecule Chains Length Organism Details
DNA DAMAGE-BINDING PROTEIN 1 A 1159 Homo sapiens Mutation: E224K
Gene Name(s): DDB1 Gene View XAP1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA DAMAGE-BINDING PROTEIN 2 B 382 Danio rerio Fragment: RESIDUES 60-423
Mutation: L180Q, W214R
Gene Name(s): ddb2 si:dkey-45f10.3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3' C 15 synthetic DAMAGED STRAND. CONTAINS CYCLOBUTANE PYRIMIDINE DIMER (CPD)
5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3' D 16 synthetic UNDAMAGED STRAND

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

C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TTD
Query on TTD
C DNA LINKING C20 H28 N4 O15 P2 DT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.347
  • R-Value Work: 0.263
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 155.64 α = 90.00
b = 227.14 β = 90.00
c = 114.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-08
  • Released Date: 2011-11-30
  • Deposition author(s): Scrima, A., Fischer, E.S., Iwai, S., Gut, H., Thoma, N.H.

Revision History

  • 2011-12-07
    Type: Citation | Details: JRNL