1XSL

Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap

Structural Biology Knowledgebase: 1XSL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.207

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XSL

Classification: TRANSFERASE / DNA

Total Structure Weight: 175713.34


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase lambda A, E, I, M 335 Homo sapiens EC#: 2.7.7.7 IUBMB 4.2.99 IUBMB
Fragment: 39 kDa catalytic C-terminal domain
Gene Name(s): POLL Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3' B, F, J, N 11 synthetic
5'-D(*GP*TP*GP*CP*GP*C)-3' C, G, K, O 6 synthetic
5'-D(P*GP*CP*CP*G)-3' D, H, L, P 4 synthetic

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

D CACODYLATE ION
dimethylarsinate (Synonym)
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B, F, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, E, I, J, M, N SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.207
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 191.50 α = 90.00
b = 98.81 β = 90.00
c = 104.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-10-19
  • Released Date: 2005-01-18
  • Deposition author(s): Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update