1RZT

Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule

Structural Biology Knowledgebase: 1RZT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.227

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1RZT

Classification: TRANSFERASE / DNA

Total Structure Weight: 172726.77


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase lambda A, E, I, M 331 Homo sapiens EC#: 2.7.7.7 IUBMB 4.2.99 IUBMB
Fragment: catalytic domain of polymerase lambda
Gene Name(s): POLL Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3' B, F, J, N 11 synthetic template DNA
5'-D(*GP*TP*GP*CP*G)-3' C, G, K, O 5 synthetic upstream primer DNA
5'-D(P*GP*CP*CP*G)-3' D, H, L, P 4 synthetic downstream primer DNA

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

M 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.227
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 191.32 α = 90.00
b = 99.03 β = 90.00
c = 104.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-12-29
  • Released Date: 2004-03-02
  • Deposition author(s): Pedersen, L.C., Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Blanco, L., Kunkel, T.A.

Revision History

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