5JLW Transcription Regulator Dna date Apr 27, 2016
title Antphd With 15bp Dna Duplex R-Monothioated At Cytidine-8
authors M.A.White, L.Zandarashvili, J.Iwahara, D.Nguyen
compound source
Molecule: Homeotic Protein Antennapedia
Chain: A, D
Engineered: Yes
Mutation: Yes
Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Antp, Cg1028
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Apgpapapapgpcp(C7r) Paptptpapgpapg)-3');
Chain: B, E
Engineered: Yes
Other_details: R-Monothiolated Phosphate At Cytidine 8

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

Molecule: Dna (5'-D(Tpcptpcptpapaptpgpgpcptptp 3');
Chain: C, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644
symmetry Space Group: P 2 2 21
R_factor 0.218 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.266 75.888 93.696 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.09 Å
ligand C7R, MPD, NI enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceStereospecific effects of oxygen-to-sulfur substitution in DNA phosphate on ion-pair dynamics and protein-DNA affinity., Nguyen D, Zandarashvili L, White MA, Iwahara J, Chembiochem. 2016 Jun 7. doi: 10.1002/cbic.201600265. PMID:27271797
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (5jlw.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (5jlw.pdb2.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 5JLW
  • CSU: Contacts of Structural Units for 5JLW
  • Structure Factors (659 Kb)
  • Retrieve 5JLW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JLW from S2C, [Save to disk]
  • Re-refined 5jlw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JLW 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 5JLW
  • 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 5jlw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jlw_E] [5jlw_B] [5jlw_A] [5jlw_C] [5jlw] [5jlw_F] [5jlw_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5JLW: [HOX ] by SMART
  • Other resources with information on 5JLW
  • Community annotation for 5JLW at PDBWiki (http://pdbwiki.org)

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