2PYL Replication, Transferase Dna date May 16, 2007
title Phi29 Dna Polymerase Complexed With Primer-Template Dna And Incoming Nucleotide Substrates (Ternary Complex)
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(Gactgcttac(2da))-3'
Chain: X
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Ctgacgaatgtaca)-3'
Chain: Y
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase
Chain: A
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 21 21 21
R_factor 0.191 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.922 78.199 157.813 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 2DA, EDO, MG, TTP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • 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] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (2pyl.pdb1.gz) 112 Kb
  • LPC: Ligand-Protein Contacts for 2PYL
  • CSU: Contacts of Structural Units for 2PYL
  • Likely Quarternary Molecular Structure file(s) for 2PYL
  • Structure Factors (563 Kb)
  • Retrieve 2PYL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PYL from S2C, [Save to disk]
  • Re-refined 2pyl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PYL 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 2PYL
  • 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 2PYL, from MSDmotif at EBI
  • Fold representative 2pyl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pyl_A] [2pyl_Y] [2pyl_X] [2pyl]
  • SWISS-PROT database: [P03680]
  • Domain organization of [DPOL_BPPH2] by SWISSPFAM
  • Domain found in 2PYL: [POLBc ] by SMART
  • Other resources with information on 2PYL
  • Community annotation for 2PYL 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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