3NAE

RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin

Structural Biology Knowledgebase: 3NAE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.194

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3NAE

Classification: TRANSFERASE / DNA

Total Structure Weight: 114714.61


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 903 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, Y567A
Gene Name(s): 43
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*CP*AP*(G35)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') T 18 synthetic Template DNA strand
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') P 13 synthetic Primer DNA strand

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

A 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
G35
Query on G35
T DNA linking C9 H16 N5 O8 P --
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.194
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.01 α = 90.00
b = 119.78 β = 90.00
c = 130.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-06-01
  • Released Date: 2010-09-15
  • Deposition author(s): Wang, M., Beckman, J., Blaha, G., Wang, J., Konigsberg, W.H.

Revision History

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