5VMD Ligase date Apr 27, 2017
title Crystal Structure Of Ubr-Box From Ubr6 In A Domain-Swapping Conformation
authors J.Munoz-Escobar, G.Kozlov, K.Gehring
compound source
Molecule: F-Box Only Protein 11
Chain: A, B, C, D
Synonym: Protein Arginine N-Methyltransferase 9, Vitiligo-A Protein 1, Vit-1, Ubr6fbxo11;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fbxo11, Fbx11, Prmt9, Vit1, Ug063h01
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.570 69.200 82.590 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand EDO, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structure of the UBR-box from UBR6/FBXO11 reveals domain swapping mediated by zinc binding., Munoz-Escobar J, Kozlov G, Gehring K, Protein Sci. 2017 Jul 10. doi: 10.1002/pro.3227. PMID:28691247
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk]
  • Biological Unit Coordinates (5vmd.pdb1.gz) 50 Kb
  • Biological Unit Coordinates (5vmd.pdb2.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 5VMD
  • CSU: Contacts of Structural Units for 5VMD
  • Structure Factors (362 Kb)
  • Retrieve 5VMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VMD from S2C, [Save to disk]
  • Re-refined 5vmd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VMD 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 5VMD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vmd_B] [5vmd_C] [5vmd_D] [5vmd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VMD
  • Community annotation for 5VMD at PDBWiki (http://pdbwiki.org)

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