4KHN

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

Structural Biology Knowledgebase: 4KHN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.168

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KHN

Classification: HYDROLASE TRANSFERASE / dna

Total Structure Weight: 230866.61


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A, B 903 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, Y567A, D714A
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') C, E 18 synthetic
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3') D, F 13 synthetic

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XG4
Query on XG4

A, B, C 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
C10 H17 N6 O12 P3
DWGAAFQEGIMTIA-KVQBGUIXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.168
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 74.26 α = 90.00
b = 119.35 β = 91.64
c = 148.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-30
  • Released Date: 2013-10-09
  • Deposition author(s): Guja, K.E., Jacewicz, A., Trzemecka, A., Plochocka, D., Yakubovskaya, E., Bebenek, A., Garcia-Diaz, M.

Revision History

  • 2013-10-23
    Type: Citation | Details: Citation update