1YBK Protein Binding date Dec 21, 2004
title Rhcc Cocrystallized With Capb
authors J.Stetefeld
compound source
Molecule: Tetrabrachion
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Staphylothermus Marinus
Organism_taxid: 2280
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31 2 1
R_factor 0.211 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.811 110.811 71.121 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.45 Å
ligand BEQ, SO4 enzyme
note 1YBK is a representative structure
related structures by homologous chain: 1FE6
Primary referenceFavourable mediation of crystal contacts by cocoamidopropylbetaine (CAPB)., Ozbek S, Muller JF, Figgemeier E, Stetefeld J, Acta Crystallogr D Biol Crystallogr 2005 Apr;61(Pt 4):477-80. Epub 2005, Mar 24. PMID:15805603
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (1ybk.pdb1.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 1YBK
  • CSU: Contacts of Structural Units for 1YBK
  • Likely Quarternary Molecular Structure file(s) for 1YBK
  • Structure Factors (656 Kb)
  • Retrieve 1YBK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YBK from S2C, [Save to disk]
  • Re-refined 1ybk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YBK 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 1YBK
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1YBK 1YBKA 1YBKB 1YBKC 1YBKD from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1YBK, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ybk_D] [1ybk] [1ybk_C] [1ybk_B] [1ybk_A]
  • SWISS-PROT database: [Q54436]
  • Domain organization of [Q54436_STAMA] by SWISSPFAM
    • Other resources with information on 1YBK
  • Community annotation for 1YBK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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