6MHA

dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Thermodynamic consequences of Tyr to Trp mutations in the cation-pi-mediated binding of trimethyllysine by the HP1 chromodomain

Krone, M.W., Albanese, K.I., Guseman, A.J., He, C.Q., Lee, G.Y., Houk, K.N., Brustad, E.M., Waters, M.L.

(2020) Chem Sci 11: 3495-3500


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heterochromatin protein 153Drosophila melanogasterMutation(s): 2 
Gene Names: Su(var)205, HP1, CG8409
UniProt
Find proteins for P05205 (Drosophila melanogaster)
Explore P05205 
Go to UniProtKB:  P05205
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05205
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
histone H3 peptide containing trimethyllysine, H3K9me36Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for P02299 (Drosophila melanogaster)
Explore P02299 
Go to UniProtKB:  P02299
Entity Groups  
UniProt GroupP02299
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.007α = 90
b = 76.695β = 90
c = 76.508γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
KYLINdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM118499

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description