3KD5

Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.

Structural Biology Knowledgebase: 3KD5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.215

Literature

Macromolecules
Sequence Display for 3KD5

Classification: TRANSFERASE / DNA

Total Structure Weight: 115777.49


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase E 913 Escherichia virus rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Fragment: RB69 gp43 exo- chimera containing elements from the fingers domain of the human cytomegalovirus DNA polymerase.
Mutation: D222A, V478W, F479V, N480S, I557M, N558A, R559L, L561V, L562T, I563C
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') T 18 synthetic
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3') P 14 synthetic

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

E PHOSPHONOFORMIC ACID
C H3 O5 P
ZJAOAACCNHFJAH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
4DG
Query on 4DG
P DNA OH 3 prime terminus C8 H12 N5 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.215
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 77.86 α = 90.00
b = 122.48 β = 90.00
c = 133.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-22
  • Released Date: 2011-04-13
  • Deposition author(s): Zahn, K.E., Doublie, S.

Revision History

  • 2015-04-15
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4