5U2T Transferase Dna date Nov 30, 2016
title Pre-Catalytic Ternary Complex Of Human Dna Polymerase Beta W Dna Substrate Incoming (-)Ftc-Tp And Ca2+.
authors R.Vyas, Z.Suo
compound source
Molecule: Dna Polymerase Beta
Chain: A
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 0.200 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
54.615 79.395 54.795 90.00 107.60 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand 1RY, ACT, CA, NA enzyme Transferase E.C. BRENDA

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] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (5u2t.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 5U2T
  • CSU: Contacts of Structural Units for 5U2T
  • Structure Factors (718 Kb)
  • Retrieve 5U2T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5U2T from S2C, [Save to disk]
  • Re-refined 5u2t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5U2T 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 5U2T
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5u2t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5u2t_P] [5u2t_T] [5u2t] [5u2t_D] [5u2t_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5U2T
  • Community annotation for 5U2T at PDBWiki (http://pdbwiki.org)

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