3NDK Transferase Dna date Jun 07, 2010
title Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp Opposi
authors M.Wang, J.Wang, W.H.Konigsberg
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Gp43
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_common: Bacteriophage Rb69
Organism_taxid: 12353
Gene: 43, Gp43
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b

Molecule: Dna (5'- D(Tpcpapgpgptpapapgpcpapgptpcpcpgpcpg)-3'
Chain: T
Engineered: Yes
Other_details: Template Dna Strand

Synthetic: Yes

Molecule: Dna (5'-D(Gpcpgpgpapcptpgpcptptpap(D
Chain: P
Engineered: Yes
Other_details: Primer Dna Strand

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.187 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.006 120.015 130.781 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CA, DCP, DOC enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


  • Primary referenceVariation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures., Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W, J Mol Biol. 2011 Jan 7. PMID:21216248
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (189 Kb) [Save to disk]
  • Biological Unit Coordinates (3ndk.pdb1.gz) 183 Kb
  • LPC: Ligand-Protein Contacts for 3NDK
  • CSU: Contacts of Structural Units for 3NDK
  • Structure Factors (1200 Kb)
  • Retrieve 3NDK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NDK from S2C, [Save to disk]
  • Re-refined 3ndk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NDK in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3NDK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3NDK, from MSDmotif at EBI
  • Fold representative 3ndk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ndk_P] [3ndk] [3ndk_T] [3ndk_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NDK: [POLBc ] by SMART
  • Other resources with information on 3NDK
  • Community annotation for 3NDK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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