3BJY Transferase Dna date Dec 05, 2007
title Catalytic Core Of Rev1 In Complex With Dna (Modified Template Guanine) And Incoming Nucleotide
authors D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal
compound source
Molecule: Dna Repair Protein Rev1
Chain: A
Fragment: Catalytic Core
Ec: 2.7.7.-
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Gene: Rev1
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Yeast
Expression_system_taxid: 4932
Expression_system_strain: Bj5464
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbj954

Molecule: Dna (5'-D(Dtpdapdap(P) Pdgpdtpdapdgpdgpdgpdgpdapdgpdgpdapdt)-3');
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Dapdtpdcpdcpdtpdcpdcpdcpdcpdtpdap(Doc))-3');
Chain: P
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.231 R_Free 0.241
length a length b length c angle alpha angle beta angle gamma
181.062 199.578 55.677 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.41 Å
ligand DCP, DOC, MG, P enzyme Transferase E.C.2.7.7 BRENDA

Primary referenceProtein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase., Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK, Structure. 2008 Feb;16(2):239-45. PMID:18275815
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (3bjy.pdb1.gz) 84 Kb
  • LPC: Ligand-Protein Contacts for 3BJY
  • CSU: Contacts of Structural Units for 3BJY
  • Likely Quarternary Molecular Structure file(s) for 3BJY
  • Structure Factors (223 Kb)
  • Retrieve 3BJY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BJY from S2C, [Save to disk]
  • Re-refined 3bjy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BJY 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 3BJY
  • 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 3BJY, from MSDmotif at EBI
  • Fold representative 3bjy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bjy_P] [3bjy_A] [3bjy] [3bjy_T]
  • SWISS-PROT database: [P12689]
  • Domain organization of [REV1_YEAST] by SWISSPFAM
  • Other resources with information on 3BJY
  • Community annotation for 3BJY 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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