5IBK Protein Binding date Feb 22, 2016
title Skp1-F-Box In Complex With A Ubiquitin Variant
authors S.Orlicky, F.Sicheri
compound source
Molecule: S-Phase Kinase-Associated Protein 1,S-Phase Kinas Associated Protein 1;
Chain: A, D
Fragment: Unp Resdiues 1-61(Deletion 37-42) And 70-163 Link Linker Ggsg,Unp Resdiues 1-61(Deletion 37-42) And 70-163 Li Linker Ggsg;
Synonym: Cyclin-Acdk2-Associated Protein P19,P19a,Organ Of Protein 2,Ocp-2,Organ Of Corti Protein II,Ocp-II,Rna Polyme Elongation Factor-Like Protein,Siii,Transcription Elongatio Polypeptide 1-Like,P19skp1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Skp1, Emc19, Ocp2, Skp1a, Tceb1l
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: F-Boxwd Repeat-Containing Protein 7
Chain: B, E
Fragment: Unp Residues 263-323
Synonym: Archipelago Homolog,Hago,F-Box And Wd-40 Domain-Co Protein 7,F-Box Protein Fbx30,Sel-10,Hcdc4;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fbxw7, Fbw7, Fbx30, Sel10
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Polyubiquitin-B
Chain: F, C
Fragment: Unp Residues 75-150
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.200 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.368 98.015 107.704 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceInhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface., Gorelik M, Orlicky S, Sartori MA, Tang X, Marcon E, Kurinov I, Greenblatt JF, Tyers M, Moffat J, Sicheri F, Sidhu SS, Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3527-32. doi:, 10.1073/pnas.1519389113. Epub 2016 Mar 14. PMID:26976582
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (195 Kb) [Save to disk]
  • Biological Unit Coordinates (5ibk.pdb1.gz) 92 Kb
  • Biological Unit Coordinates (5ibk.pdb2.gz) 94 Kb
  • CSU: Contacts of Structural Units for 5IBK
  • Structure Factors (471 Kb)
  • Retrieve 5IBK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IBK from S2C, [Save to disk]
  • Re-refined 5ibk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IBK 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 5IBK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ibk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ibk_A] [5ibk_E] [5ibk_B] [5ibk_F] [5ibk] [5ibk_D] [5ibk_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IBK: [FBOX] [Skp1] [UBQ ] by SMART
  • Other resources with information on 5IBK
  • Community annotation for 5IBK at PDBWiki (http://pdbwiki.org)

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