4RT2 Transferase Dna date Nov 12, 2014
title Ternary Complex Crystal Structure Of Dna Polymerase Beta Wit Beta)-Ch2-(Beta,Gamma)-Nh-Dttp
authors V.K.Batra, S.H.Wilson
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: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl11

Molecule: Dna (5'-D(Cpcpgpapcpapgpcpgpcpaptpcp 3');
Chain: T
Synonym: Template Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgp(Doc))-3')
Chain: P
Synonym: Primer Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Synonym: Downstream Primer Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.176 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.587 79.409 55.315 90.00 107.27 90.00
method X-Ray Diffractionresolution 1.92 Å
ligand CL, DOC, MG, N6T, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceTwo Scaffolds from Two Flips: (alpha,beta)/(beta,gamma) CH2/NH "Met-Im" Analogues of dTTP., Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson SH, Goodman MF, McKenna CE, Org Lett. 2015 Jun 5;17(11):2586-9. doi: 10.1021/acs.orglett.5b00799. Epub 2015, May 13. PMID:25970636
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (4rt2.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 4RT2
  • CSU: Contacts of Structural Units for 4RT2
  • Structure Factors (281 Kb)
  • Retrieve 4RT2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4RT2 from S2C, [Save to disk]
  • Re-refined 4rt2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RT2 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 4RT2
  • 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 4rt2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rt2_T] [4rt2_P] [4rt2] [4rt2_D] [4rt2_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4RT2: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4RT2
  • Community annotation for 4RT2 at PDBWiki (http://pdbwiki.org)

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