2P5G Transferase Dna date Mar 15, 2007
title Crystal Structure Of Rb69 Gp43 In Complex With Dna With Damp An Abasic Site Analog In A 21mer Template
authors K.E.Zahn, H.Belrhali, S.S.Wallace, S.Doublie
compound source
Molecule: Template Dna
Chain: E, G, I, K
Engineered: Yes
Synthetic: Yes

Molecule: Primer Dna
Chain: F, H, J, L
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase
Chain: A, B, C, D
Synonym: Gp43
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Enterobacteria Phage Rb69
Organism_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1 21 1
R_factor 0.234 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
131.628 122.272 163.871 90.00 96.45 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 3DR, MSE enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


  • Primary referenceCaught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide., Zahn KE, Belrhali H, Wallace SS, Doublie S, Biochemistry. 2007 Sep 18;46(37):10551-61. Epub 2007 Aug 24. PMID:17718515
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (597 Kb) [Save to disk]
  • Biological Unit Coordinates (2p5g.pdb1.gz) 161 Kb
  • Biological Unit Coordinates (2p5g.pdb2.gz) 138 Kb
  • Biological Unit Coordinates (2p5g.pdb3.gz) 162 Kb
  • Biological Unit Coordinates (2p5g.pdb4.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 2P5G
  • CSU: Contacts of Structural Units for 2P5G
  • Likely Quarternary Molecular Structure file(s) for 2P5G
  • Structure Factors (3429 Kb)
  • Retrieve 2P5G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2P5G from S2C, [Save to disk]
  • Re-refined 2p5g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2P5G 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 2P5G
  • 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 2P5G, from MSDmotif at EBI
  • Fold representative 2p5g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2p5g_G] [2p5g] [2p5g_F] [2p5g_E] [2p5g_H] [2p5g_I] [2p5g_D] [2p5g_A] [2p5g_K] [2p5g_C] [2p5g_J] [2p5g_B] [2p5g_L]
  • SWISS-PROT database: [Q38087]
  • Domain organization of [DPOL_BPR69] by SWISSPFAM
  • Domain found in 2P5G: [POLBc ] by SMART
  • Other resources with information on 2P5G
  • Community annotation for 2P5G 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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