6BVA Protein Binding date Dec 12, 2017
title Ubiquitin Variant (Ubv.Fl10.1) Bound To A Human Skp1-Fbl10 F Complex.
authors N.Manczyk, F.Sicheri
compound source
Molecule: S-Phase Kinase-Associated Protein 1
Chain: D, C
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
Expression_system_taxid: 562

Molecule: Lysine-Specific Demethylase 2b
Chain: E, F
Synonym: Cxxc-Type Zinc Finger Protein 2,F-Box And Leucine- Repeat Protein 10,F-Box Protein Fbl10,F-Boxlrr-Repeat Prot Jmjc Domain-Containing Histone Demethylation Protein 1b,Jum Domain-Containing Emsy-Interactor Methyltransferase Motif P Protein Jemma,Protein-Containing Cxxc Domain 2,[Histone-H3] Demethylase 1b;
Ec: 1.14.11.27
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm2b, Cxxc2, Fbl10, Fbxl10, Jhdm1b, Pccx2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polyubiquitin-B
Chain: B, A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.360 81.793 128.685 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.66 Å
ligand
enzyme Oxidoreductase E.C.1.14.11.27 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
D, C


Primary referenceA Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases., Gorelik M, Manczyk N, Pavlenco A, Kurinov I, Sidhu SS, Sicheri F, Structure. 2018 Jun 26. pii: S0969-2126(18)30210-7. doi:, 10.1016/j.str.2018.06.004. PMID:30033217
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk]
  • Biological Unit Coordinates (6bva.pdb1.gz) 87 Kb
  • Biological Unit Coordinates (6bva.pdb2.gz) 92 Kb
  • CSU: Contacts of Structural Units for 6BVA
  • Structure Factors (269 Kb)
  • Retrieve 6BVA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6BVA from S2C, [Save to disk]
  • View 6BVA 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 6BVA
  • 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 6bva from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6bva_D] [6bva_A] [6bva_E] [6bva_B] [6bva_C] [6bva_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6BVA
  • Community annotation for 6BVA at PDBWiki (http://pdbwiki.org)

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