6YCS Transcription date Mar 19, 2020
title Human Transcription Cofactor Pc4 Dna-Binding Domain In Compl Full Phosphorothioate 5-10-5 2'-O-Methyl Dna Gapmer Antisen Oligonucleotide.
authors M.Hyjek-Skladanowska, T.A.Vickers, A.Napiorkowska, B.Anderson, M.Tanowitz, S.T.Crooke, X.Liang, P.P.Seth, M.Nowotny
compound source
Molecule: Pc4 Protein
Chain: A, B, C, D
Synonym: Sub1 Homolog (S. Cerevisiae),Isoform Cra_a,Cdna,Fl Highly Similar To Homo Sapiens Sub1 Homolog (S. Cerevisiae) Mrna;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pc4, Sub1, Hcg_1781938
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Dna (5'-D(P(Okq))-D(P(Okt))-R(P(Rfj))-D((Okq) P(As)P(Gs)P(Okn)P(Okn)P(Pst)P(Okn)P(Pst)P(Gs)P(Gs) P(Okt)P(Okt))-3');
Chain: E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(P(Okq))-D(P(Okt))-R(P(Rfj))-D((Okq) P(As)P(Gs)P(Okn)P(Okn)P(Pst)P(Okn)P(Pst)P(Gs)P(Gs) P(Okt)P(Okt))-3');
Chain: F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 43 21 2
R_factor 0.238 R_Free 0.318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.143 102.143 83.813 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.05 Å
ligand GS, NA, OKN, OKQ, OKT, PPS, PST, RFJ, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (6ycs.pdb1.gz) 112 Kb
  • LPC: Ligand-Protein Contacts for 6YCS
  • CSU: Contacts of Structural Units for 6YCS
  • Structure Factors (51 Kb)
  • Retrieve 6YCS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YCS from S2C, [Save to disk]
    • View 6YCS 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 6YCS
  • 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: [6ycs_C] [6ycs_F] [6ycs_A] [6ycs_B] [6ycs_E] [6ycs_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6YCS
  • Community annotation for 6YCS at PDBWiki (http://pdbwiki.org)

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