3PY8 Transferase Dna date Dec 12, 2010
title Crystal Structure Of A Mutant Of The Large Fragment Of Dna P I From Thermus Aquaticus In A Closed Ternary Complex With D Ddctp
authors A.Schnur, A.Marx, W.Welte, K.Diederichs
compound source
Molecule: Dna Polymerase I
Chain: A
Fragment: Dna Polymerase I Large Fragment
Synonym: Taq Polymerase 1
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Gene: Pola, Pol1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Gold(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pask-Iba37plus

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

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 31 2 1
R_factor 0.169 R_Free 0.199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.610 108.610 90.570 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.74 Å
ligand DCT, DOC, GOL, MG, MN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceLearning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity., Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W, Diederichs K, Marx A, Chembiochem. 2011 Apr 8. doi: 10.1002/cbic.201000783. PMID:21480455
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (205 Kb) [Save to disk]
  • Biological Unit Coordinates (3py8.pdb1.gz) 196 Kb
  • LPC: Ligand-Protein Contacts for 3PY8
  • CSU: Contacts of Structural Units for 3PY8
  • Structure Factors (520 Kb)
  • Retrieve 3PY8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PY8 from S2C, [Save to disk]
  • Re-refined 3py8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PY8 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 3PY8
  • 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
  • 3D motif for 3PY8, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3py8] [3py8_C] [3py8_A] [3py8_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PY8: [POLAc ] by SMART
  • Other resources with information on 3PY8
  • Community annotation for 3PY8 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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