5TBA Transferase Dna date Sep 11, 2016
title Postcatalytic Ternary Complex Of Human Dna Polymerase Beta W Dna Substrate, Incorporated (-)3tc And Ppi.
authors R.Vyas, Z.Suo
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7,4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: 5-Mer Phosphorylated Downstream Primer
Chain: D
Engineered: Yes
Other_details: Synthetic Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 10-Mer Primer
Chain: P
Engineered: Yes
Other_details: Synthetic Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 16-Mer Template
Chain: T
Engineered: Yes
Other_details: Synthetic Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.205 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.697 79.325 54.947 90.00 107.03 90.00
method X-Ray Diffractionresolution 2.49 Å
ligand 42E, NA, PPV enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase., Reed AJ, Vyas R, Raper AT, Suo Z, J Am Chem Soc. 2017 Jan 11;139(1):465-471. doi: 10.1021/jacs.6b11258. Epub 2016, Dec 27. PMID:27959534
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (5tba.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 5TBA
  • CSU: Contacts of Structural Units for 5TBA
  • Structure Factors (262 Kb)
  • Retrieve 5TBA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TBA from S2C, [Save to disk]
  • Re-refined 5tba structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5TBA 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 5TBA
  • 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
  • Fold representative 5tba from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tba_D] [5tba_A] [5tba] [5tba_T] [5tba_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5TBA
  • Community annotation for 5TBA at PDBWiki (http://pdbwiki.org)

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