6HGT

Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure-based design of selective, histone substrate-based inhibitors of histone lysine demethylases 4 (KDM4) subfamily

Maw, J.Le Bihan, Y.V.Bavetsias, V.Blagg, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 4AA, B, C, D360Homo sapiensMutation(s): 0 
Gene Names: KDM4AJHDM3AJMJD2JMJD2AKIAA0677
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens)
Explore O75164 
Go to UniProtKB:  O75164
PHAROS:  O75164
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3E, F, G, H15Homo sapiensMutation(s): 1 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.44α = 90
b = 103.41β = 99.63
c = 144.52γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC347/A18364

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release