3SUP

RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (GC rich sequence)

Structural Biology Knowledgebase: 3SUP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.200

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3SUP

Classification: TRANSFERASE / DNA

Total Structure Weight: 114095.36


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
5'-D(P*CP*(2PR)P*TP*CP*GP*CP*CP*GP*CP*CP*GP*CP*GP*CP*GP*G)-3' T 16 synthetic template
5'-D(*CP*GP*CP*GP*CP*GP*GP*CP*GP*GP*CP*GP*(2DA))-3' P 13 synthetic primer

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

A 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-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
2PR
Query on 2PR
T DNA LINKING C10 H14 N5 O6 P DG
2DA
Query on 2DA
P DNA LINKING C10 H14 N5 O5 P DA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.200
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 74.76 α = 90.00
b = 120.36 β = 90.00
c = 130.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-07-11
  • Released Date: 2011-11-09
  • Deposition author(s): Xia, S., Konigsberg, W.H., Wang, J.

Revision History

  • 2011-11-30
    Type: Citation | Details: Citation update
  • 2011-11-16
    Type: Citation | Details: Citation update