1C03 Signaling Protein date Jul 14, 1999
title Crystal Structure Of Ypd1p (Triclinic Form)
authors H.K.Song, J.Y.Lee, M.G.Lee, S.W.Suh
compound source
Molecule: Hypothetical Protein Ydl235c
Chain: A, B, C, D
Synonym: Ypd1p
Engineered: Yes
Mutation: Yes
Other_details: Triclinic Form
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-22b
symmetry Space Group: P 1
R_factor 0.206 R_Free 0.248
length a length b length c angle alpha angle beta angle gamma
66.343 66.480 66.491 106.37 106.66 115.33
method X-Ray Diffractionresolution 2.30 Å
related structures by homologous chain: 1OXB, 1OXK
A, D, C, B
  • histidine phosphotransfer ki...

  • Primary referenceInsights into eukaryotic multistep phosphorelay signal transduction revealed by the crystal structure of Ypd1p from Saccharomyces cerevisiae., Song HK, Lee JY, Lee MG, Moon J, Min K, Yang JK, Suh SW, J Mol Biol 1999 Nov 5;293(4):753-61. PMID:10543964
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (1c03.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (1c03.pdb2.gz) 28 Kb
  • Biological Unit Coordinates (1c03.pdb3.gz) 29 Kb
  • Biological Unit Coordinates (1c03.pdb4.gz) 28 Kb
  • CSU: Contacts of Structural Units for 1C03
  • Likely Quarternary Molecular Structure file(s) for 1C03
  • Structure Factors (307 Kb)
  • Retrieve 1C03 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1C03 from S2C, [Save to disk]
  • Re-refined 1c03 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1C03 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 1C03
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1C03, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1c03a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1c03b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1c03c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1c03d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1c03 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1c03_C] [1c03] [1c03_A] [1c03_B] [1c03_D]
  • SWISS-PROT database: [Q07688]
  • Domain organization of [YPD1_YEAST] by SWISSPFAM
  • Domain found in 1C03: [HPT ] by SMART
  • Other resources with information on 1C03
  • Community annotation for 1C03 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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