5V1N Transferase Dna, Ligase Dna date Mar 02, 2017
title Dna Polymerase Beta Substrate Complex With 8-Oxog:A At The P Terminus And Incoming Dctp
authors B.D.Freudenthal, M.A.Schaich, A.M.Whitaker, M.R.Smith
compound source
Molecule: Dna (5'-D(Cpcpgpapcpgpapcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgp(8og))-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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
symmetry Space Group: P 1 21 1
R_factor 0.181 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.546 79.225 55.536 90.00 107.32 90.00
method X-Ray Diffractionresolution 2.01 Å
ligand 8OG, CA, CL, DCP, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCapturing a mammalian DNA polymerase extending from an oxidized nucleotide., Whitaker AM, Smith MR, Schaich MA, Freudenthal BD, Nucleic Acids Res. 2017 Apr 26. doi: 10.1093/nar/gkx293. PMID:28449123
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (5v1n.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 5V1N
  • CSU: Contacts of Structural Units for 5V1N
  • Structure Factors (343 Kb)
  • Retrieve 5V1N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V1N from S2C, [Save to disk]
  • Re-refined 5v1n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5V1N 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 5V1N
  • 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 5v1n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v1n_D] [5v1n_T] [5v1n_A] [5v1n_P] [5v1n]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5V1N
  • Community annotation for 5V1N at PDBWiki (http://pdbwiki.org)

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