2PYJ Replication, Transferase Dna date May 16, 2007
title Phi29 Dna Polymerase Complexed With Primer-Template Dna And Nucleotide Substrates (Ternary Complex)
authors A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lazaro, M.De Vega, L.Bla M.Salas, T.A.Steitz
compound source
Molecule: 5'-D(Gactgctta(Doc)-3'
Chain: X, Q, J
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Acacgtaagcagtc)-3'
Chain: Y, R, K
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase
Chain: A, B
Synonym: Early Protein Gp2
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Bacillus Phage Phi29
Organism_taxid: 10756
Gene: 2, Gp2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.189 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.835 114.667 104.761 90.00 94.07 90.00
method X-Ray Diffractionresolution 2.03 Å
ligand DGT, DOC, EDO, MG, MN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity


  • Primary referenceStructures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases., Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, EMBO J. 2007 Jul 5;. PMID:17611604
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (245 Kb) [Save to disk]
  • Biological Unit Coordinates (2pyj.pdb1.gz) 117 Kb
  • Biological Unit Coordinates (2pyj.pdb2.gz) 115 Kb
  • Biological Unit Coordinates (2pyj.pdb3.gz) 15 Kb
  • LPC: Ligand-Protein Contacts for 2PYJ
  • CSU: Contacts of Structural Units for 2PYJ
  • Likely Quarternary Molecular Structure file(s) for 2PYJ
  • Structure Factors (1627 Kb)
  • Retrieve 2PYJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PYJ from S2C, [Save to disk]
  • Re-refined 2pyj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PYJ 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 2PYJ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2PYJ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pyj_R] [2pyj_Q] [2pyj_B] [2pyj] [2pyj_K] [2pyj_Y] [2pyj_J] [2pyj_A] [2pyj_X]
  • SWISS-PROT database: [P03680]
  • Domain organization of [DPOL_BPPH2] by SWISSPFAM
  • Domain found in 2PYJ: [POLBc ] by SMART
  • Other resources with information on 2PYJ
  • Community annotation for 2PYJ 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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