1DE9

HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION

Structural Biology Knowledgebase: 1DE9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 1DE9

Classification: LYASE / DNA

Total Structure Weight: 73142.80


Macromolecule Entities
Molecule Chains Length Organism Details
MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE A, B 276 Homo sapiens EC#: 3.1 IUBMB 4.2.99.18 IUBMB
Fragment: APE1
Gene Name(s): APEX1 Gene View APE APE1 APEX APX HAP1 Gene View REF1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-d(*CP*TP*AP*C)-3' U, X 4 synthetic
5'-d(P*(3DR)P*GP*AP*TP*C)-3' V, Y 5 synthetic
5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3' W, Z 9 synthetic

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

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
V, Y DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.183
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 90.06 α = 90.00
b = 98.35 β = 90.00
c = 101.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-11-13
  • Released Date: 2000-02-02
  • Deposition author(s): Mol, C.D., Izumi, T., Mitra, S., Tainer, J.A.

Revision History

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