3M8R Transferase Dna date Mar 19, 2010
title Crystal Structure Of The Large Fragment Of Dna Polymerase I Thermus Aquaticus In A Closed Ternary Complex With Trapped Ethylated Dttp
authors K.Diederichs, A.Marx, K.Betz
compound source
Molecule: Dna Polymerase I, Thermostable
Chain: A
Fragment: Klenow Fragment
Synonym: Taq Polymerase 1
Engineered: Yes
Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Gene: Pola, Pol1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-21b

Molecule: Dna (5'-D(Gpapcpcpapcpgpgpcpgpcp(Doc)
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Apapapapgpgpcpgpcpcpgptpgp 3');
Chain: C
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 31 2 1
R_factor 0.180 R_Free 0.221
length a length b length c angle alpha angle beta angle gamma
108.789 108.789 90.520 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand 15P, ACT, DOC, GOL, HXZ, MG enzyme Transferase E.C. BRENDA
Primary referenceStructures of DNA Polymerases Caught Processing Size-Augmented Nucleotide Probes., Betz K, Streckenbach F, Schnur A, Exner T, Welte W, Diederichs K, Marx A, Angew Chem Int Ed Engl. 2010 Jun 22. PMID:20572212
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (220 Kb) [Save to disk]
  • Biological Unit Coordinates (3m8r.pdb1.gz) 212 Kb
  • LPC: Ligand-Protein Contacts for 3M8R
  • CSU: Contacts of Structural Units for 3M8R
  • Structure Factors (242 Kb)
  • Retrieve 3M8R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3M8R from S2C, [Save to disk]
  • Re-refined 3m8r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3M8R 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 3M8R
  • 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 3M8R, from MSDmotif at EBI
  • Fold representative 3m8r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3m8r] [3m8r_A] [3m8r_C] [3m8r_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3M8R: [POLAc ] by SMART
  • Other resources with information on 3M8R
  • Community annotation for 3M8R at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science