3PR5 Transferase Dna date Nov 29, 2010
title Dpo4 Y12a Mutant Incorporating Adp Opposite Template Dt
authors K.N.Kirouac, H.Ling
compound source
Molecule: Dna Polymerase Iv
Chain: B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Gpgpgpgpgpapapgpgpapcptpc)
Chain: P
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Tptpcpaptpgpapgptpcpcptptpcpcpcpcpc)-3'
Chain: T
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.228 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.607 101.993 52.288 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ATP, CA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceStructural Mechanism of Ribonucleotide Discrimination by a Y-Family DNA Polymerase., Kirouac KN, Suo Z, Ling H, J Mol Biol. 2011 Feb 3. PMID:21295588
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (3pr5.pdb1.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 3PR5
  • CSU: Contacts of Structural Units for 3PR5
  • Structure Factors (412 Kb)
  • Retrieve 3PR5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PR5 from S2C, [Save to disk]
  • Re-refined 3pr5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PR5 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 3PR5
  • 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 3PR5, from MSDmotif at EBI
  • Fold representative 3pr5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pr5_P] [3pr5] [3pr5_B] [3pr5_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3PR5
  • Community annotation for 3PR5 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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