5NLF Ligase date Apr 04, 2017
title Crystal Structure Of Zn2.7-E16v Human Ubiquitin (Hub) Mutant From A Solution 100 Mm Zinc Acetate1.3 Mm E16v Hub
authors S.Fermani, G.Falini
compound source
Molecule: Polyubiquitin-C
Chain: A, B, C
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.156 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.410 50.530 93.680 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand ACT, ZN enzyme
Primary referenceAggregation pathways of native-like ubiquitin promoted by single-point mutation, metal ion concentration and dielectric constant of the medium., Fermani S, Calvaresi M, Mangini V, Falini G, Bottoni A, Natile G, Arnesano F, Chemistry. 2017 Dec 20. doi: 10.1002/chem.201705543. PMID:29266436
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (5nlf.pdb1.gz) 15 Kb
  • Biological Unit Coordinates (5nlf.pdb2.gz) 15 Kb
  • Biological Unit Coordinates (5nlf.pdb3.gz) 15 Kb
  • LPC: Ligand-Protein Contacts for 5NLF
  • CSU: Contacts of Structural Units for 5NLF
  • Structure Factors (884 Kb)
  • Retrieve 5NLF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NLF from S2C, [Save to disk]
  • Re-refined 5nlf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5NLF 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 5NLF
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5nlf] [5nlf_C] [5nlf_B] [5nlf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5NLF
  • Community annotation for 5NLF at PDBWiki (http://pdbwiki.org)

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