5R09 Splicing date Mar 30, 2020
title Pandda Analysis Group Deposition -- Aar2rnaseh In Complex W Fragment F2x-Entry B03, Dmso-Free
authors J.Wollenhaupt, A.Metz, T.Barthel, G.M.A.Lima, A.Heine, U.Mueller, M.S.Weiss
compound source
Molecule: Pre-Mrna-Splicing Factor 8
Chain: A
Fragment: Yprp8 Rnaseh (Unp Residues 1836-2096)
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Prp8, Dbf3, Dna39, Rna8, Slt21, Usa2, Yhr165c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: A1 Cistron-Splicing Factor Aar2
Chain: B
Fragment: Gama - Aar2(1-152) - Sssss - Aar2(171-317)
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Aar2, Ybl074c, Ybl06.06, Ybl0611
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.203 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.612 81.915 93.845 90.00 108.42 90.00
method X-Ray Diffractionresolution 1.56 Å
ligand SYG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceF2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening., Wollenhaupt J, Metz A, Barthel T, Lima GMA, Heine A, Mueller U, Klebe G, Weiss MS, Structure. 2020 Jun 2;28(6):694-706.e5. doi: 10.1016/j.str.2020.04.019. Epub 2020, May 14. PMID:32413289
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (5r09.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 5R09
  • CSU: Contacts of Structural Units for 5R09
  • Structure Factors (2328 Kb)
  • Retrieve 5R09 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5R09 from S2C, [Save to disk]
    • View 5R09 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 5R09
  • 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: [5r09_A] [5r09_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5R09
  • Community annotation for 5R09 at PDBWiki (http://pdbwiki.org)

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