1X9N

Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA

Structural Biology Knowledgebase: 1X9N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.235

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1X9N

Classification: Ligase / DNA

Total Structure Weight: 94110.48


Macromolecule Entities
Molecule Chains Length Organism Details
DNA ligase I A 688 Homo sapiens EC#: 6.5.1.1 IUBMB
Mutation: M308M, M393M, M480M, M501M, M543M, M723M
Gene Name(s): LIG1 Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
dideoxy terminated DNA B 13 synthetic
5'-phosphorylated DNA C 15 synthetic
template DNA D 28 synthetic

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

C ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
B DNA LINKING C9 H14 N3 O6 P DC
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.235
  • Space Group: P 63
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 161.89 α = 90.00
b = 161.89 β = 90.00
c = 88.46 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-08-23
  • Released Date: 2004-11-30
  • Deposition author(s): Pascal, J.M., O'Brien, P.J., Tomkinson, A.E., Ellenberger, T.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4