5YBV Cell Adhesion date Sep 05, 2017
title The Structure Of The Kank2 Ankyrin Domain With The Kif21a Pe
authors Q.Guo, S.Liao, J.Min, C.Xu, Structural Genomics Consortium (Sgc)
compound source
Molecule: Kn Motif And Ankyrin Repeat Domain-Containing Pro
Chain: A
Fragment: Unp Residues 578-832
Synonym: Ankyrin Repeat Domain-Containing Protein 25,Matrix Remodeling-Associated Protein 3,Src-1-Interacting Protein,S Interacting Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kank2, Ankrd25, Kiaa1518, Mxra3, Sip
Expression_system: Escherichia Coli-Thermus Thermophilus Sh Vector Ptrh1t;
Expression_system_taxid: 1085940

Molecule: Kn Motif And Ankyrin Repeat Domain-Containing Pro
Chain: B
Fragment: Unp Residues 578-832
Synonym: Ankyrin Repeat Domain-Containing Protein 25,Matrix Remodeling-Associated Protein 3,Src-1-Interacting Protein,S Interacting Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kank2, Ankrd25, Kiaa1518, Mxra3, Sip
Expression_system: Escherichia Coli-Thermus Thermophilus Sh Vector Ptrh1t;
Expression_system_taxid: 1085940

Molecule: Kinesin-Like Protein Kif21a
Chain: C, D
Fragment: Unp Residues 1146-1167
Synonym: Kinesin-Like Protein Kif2,Renal Carcinoma Antigen
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor 0.188 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.956 52.834 53.478 73.02 89.67 84.91
method X-Ray Diffractionresolution 2.12 Å
Primary referenceStructural basis for the recognition of kinesin family member 21A (KIF21A) by the ankyrin domains of KANK1 and KANK2 proteins., Guo Q, Liao S, Zhu Z, Li Y, Li F, Xu C, J Biol Chem. 2017 Nov 28. pii: M117.817494. doi: 10.1074/jbc.M117.817494. PMID:29183992
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (5ybv.pdb1.gz) 166 Kb
  • CSU: Contacts of Structural Units for 5YBV
  • Structure Factors (532 Kb)
  • Retrieve 5YBV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YBV from S2C, [Save to disk]
  • View 5YBV 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 5YBV
  • 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
  • Fold representative 5ybv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ybv_D] [5ybv_A] [5ybv_B] [5ybv_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YBV
  • Community annotation for 5YBV at PDBWiki (http://pdbwiki.org)

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