1Q9X

Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.215

Literature

Macromolecules
Sequence Display for 1Q9X

Classification: Transferase replication / DNA

Total Structure Weight: 461118.50


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A, B, C, D 903 Escherichia virus rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-GCGGACTGCTTAC(dideoxycytidine)-3' E, F, G, H 18 synthetic
5'-AC(tetrahydrofuran)GGTAAGCAGTCCGCGG-3' I, J, K, L 13 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DGP
Query on DGP

F, G, H, K, L 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DOC
Query on DOC

I, J, K, L 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O6 P
RAJMXAZJKUGYGW-POYBYMJQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3DR
Query on 3DR

E, F, G, H 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
ABASIC DIDEOXYRIBOSE (Synonym)
C5 H11 O6 P
BVOBPNSQIRMLCA-CRCLSJGQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.215
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 131.95 α = 90.00
b = 122.24 β = 96.85
c = 165.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-08-26
  • Released Date: 2004-04-27
  • Deposition author(s): Freisinger, E., Grollman, A.P., Miller, H., Kisker, C.

Revision History

  • Version 1_0: 2004-04-27

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance