4ZG1

Crystal structure of a nanobody raised against KDM5B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and binding properties of a cameloid nanobody raised against KDM5B.

Wiuf, A.Kristensen, L.H.Kristensen, O.Dorosz, J.Jensen, J.Gajhede, M.

(2015) Acta Crystallogr.,Sect.F 71: 1235-1241

  • DOI: 10.1107/S2053230X1501537X

  • PubMed Abstract: 
  • The histone demethylase KDM5B is considered to be a promising target for anticancer therapy. Single-chain antibodies from llama (nanobodies) have been raised to aid in crystallization and structure determination of this enzyme. The antigen-binding pr ...

    The histone demethylase KDM5B is considered to be a promising target for anticancer therapy. Single-chain antibodies from llama (nanobodies) have been raised to aid in crystallization and structure determination of this enzyme. The antigen-binding properties of 15 of these nanobodies have been characterized. The crystal structure of one of these (NB17) has been determined to a resolution of 1.85 Å. NB17 crystallizes in space group P4322 with six molecules in the asymmetric unit. The six molecules in the asymmetric unit pack as an entity with approximate D3 symmetry with interactions mediated by the CDR loops, which could act as a crystallization nucleus. NB17 does not bind to monomeric KDM5B residues 1-820, but is found to bind to aggregates formed after incubation at 310 K.


    Organizational Affiliation

    Department of Drug Design and Pharmacology, University of Copenhagen, 2200 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NB17
A, B, C, D, E, F
117N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.520α = 90.00
b = 91.520β = 90.00
c = 184.590γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-10-21
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection