1NEX Ligase, Cell Cycle date Dec 12, 2002
title Crystal Structure Of Scskp1-Sccdc4-Cpd Peptide Complex
authors S.Orlicky, X.Tang, A.Willems, M.Tyers, F.Sicheri
compound source
Molecule: Centromere Dna-Binding Protein Complex Cbf3 Subun
Chain: A, C
Fragment: Residues 36-63 Deleted
Synonym: Scskp1, Suppressor Of Kinetochore Protein 1
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Cbf3d Or Skp1 Or Ydr328c Or D9798.14
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproex Htb

Molecule: Cdc4 Protein
Chain: B, D
Fragment: Residues 601-604 And 609-624 Deleted
Synonym: Sccdc4
Engineered: Yes
Mutation: Yes
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

Molecule: Gll(Tpo)Ppqsg
Chain: E, F
Engineered: Yes
symmetry Space Group: P 32
R_factor 0.239 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.669 107.669 168.300 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand MSE, TPO enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceStructural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase., Orlicky S, Tang X, Willems A, Tyers M, Sicheri F, Cell 2003 Jan 24;112(2):243-56. PMID:12553912
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (198 Kb) [Save to disk]
  • Biological Unit Coordinates (1nex.pdb1.gz) 95 Kb
  • Biological Unit Coordinates (1nex.pdb2.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 1NEX
  • CSU: Contacts of Structural Units for 1NEX
  • Likely Quarternary Molecular Structure file(s) for 1NEX
  • Structure Factors (935 Kb)
  • Retrieve 1NEX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NEX from S2C, [Save to disk]
  • Re-refined 1nex structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1NEX 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 1NEX
  • 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
  • 3D motif for 1NEX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nexa1, region A:116-185 [Jmol] [rasmolscript] [script source]
        - Domain d1nexa2, region A:4-103 [Jmol] [rasmolscript] [script source]
        - Domain d1nexb1, region B:270-369 [Jmol] [rasmolscript] [script source]
        - Domain d1nexb2, region B:370-744 [Jmol] [rasmolscript] [script source]
        - Domain d1nexc1, region C:116-186 [Jmol] [rasmolscript] [script source]
        - Domain d1nexc2, region C:4-103 [Jmol] [rasmolscript] [script source]
        - Domain d1nexd1, region D:270-369 [Jmol] [rasmolscript] [script source]
        - Domain d1nexd2, region D:370-744 [Jmol] [rasmolscript] [script source]
  • 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: [1nex] [1nex_D] [1nex_C] [1nex_E] [1nex_F] [1nex_B] [1nex_A]
  • SWISS-PROT database: [P07834] [P52286]
  • Domain organization of [CDC4_YEAST] [SKP1_YEAST] by SWISSPFAM
  • Domains found in 1NEX: [FBOX] [Skp1] [WD40 ] by SMART
    • Other resources with information on 1NEX
  • Community annotation for 1NEX 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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