5U2S Transferase Dna date Nov 30, 2016
title Pre-Catalytic Ternary Complex Of Human Dna Polymerase Beta W Dna Substrate Incoming (-)3tc-Tp And Ca2+.
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
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 10- Mer Primer
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 16- Mer Template
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.230 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.630 79.450 55.170 90.00 106.66 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 1RZ, ACT, CA, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for the D-stereoselectivity of human DNA polymerase beta., Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer PC, Suo Z, Nucleic Acids Res. 2017 Apr 10. doi: 10.1093/nar/gkx252. PMID:28402499
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (5u2s.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 5U2S
  • CSU: Contacts of Structural Units for 5U2S
  • Structure Factors (1338 Kb)
  • Retrieve 5U2S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5U2S from S2C, [Save to disk]
  • Re-refined 5u2s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5U2S 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 5U2S
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5u2s_D] [5u2s_P] [5u2s_A] [5u2s] [5u2s_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5U2S
  • Community annotation for 5U2S at PDBWiki (http://pdbwiki.org)

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