5WNY Dna Ligase Dna, Transferase date Aug 01, 2017
title Dna Polymerase Beta Substrate Complex With Incoming 5-Fdutp
authors M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal
compound source
Molecule: Dna (5'-D(Cpcpgpapcpapgpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-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
50.480 79.747 55.570 90.00 107.23 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand
enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues., Schaich MA, Smith MR, Cloud AS, Holloran SM, Freudenthal BD, Chem Res Toxicol. 2017 Sep 1. doi: 10.1021/acs.chemrestox.7b00173. PMID:28862449
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (5wny.pdb1.gz) 73 Kb
  • CSU: Contacts of Structural Units for 5WNY
  • Structure Factors (312 Kb)
  • Retrieve 5WNY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5WNY from S2C, [Save to disk]
  • View 5WNY 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 5WNY
  • 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 5wny from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5wny_D] [5wny_A] [5wny_T] [5wny_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5WNY
  • Community annotation for 5WNY at PDBWiki (http://pdbwiki.org)

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