2PY5 Replication, Transferase Dna date May 15, 2007
title Phi29 Dna Polymerase Complexed With Single-Stranded Dna
authors A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lazaro, M.De Vega, L.Blanco, M.Salas, T.A.Steitz
compound source
Molecule: 5'-D(Ggacttt)-3'
Chain: J, Y, D, E, L
Engineered: Yes
Synthetic: Yes

Molecule: Dna Polymerase
Chain: A, B
Synonym: Early Protein Gp2
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 0.164 R_Free 0.194
length a length b length c angle alpha angle beta angle gamma
54.195 200.178 66.989 90.00 109.40 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand EDO enzyme Transferase E.C. BRENDA
note 2PY5 is a representative structure
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] (235 Kb) [Save to disk]
  • Biological Unit Coordinates (2py5.pdb1.gz) 120 Kb
  • Biological Unit Coordinates (2py5.pdb2.gz) 112 Kb
  • LPC: Ligand-Protein Contacts for 2PY5
  • CSU: Contacts of Structural Units for 2PY5
  • Likely Quarternary Molecular Structure file(s) for 2PY5
  • Structure Factors (2507 Kb)
  • Retrieve 2PY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PY5 from S2C, [Save to disk]
  • Re-refined 2py5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PY5 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 2PY5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2PY5, from MSDmotif at EBI
  • Fold representative 2py5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2py5_J] [2py5] [2py5_E] [2py5_A] [2py5_Y] [2py5_B] [2py5_D] [2py5_L]
  • SWISS-PROT database: [P03680]
  • Domain organization of [DPOL_BPPH2] by SWISSPFAM
  • Domain found in 2PY5: [POLBc ] by SMART
  • Other resources with information on 2PY5
  • Community annotation for 2PY5 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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