6HGT | pdb_00006hgt

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

• PDB DOI: https://doi.org/10.2210/pdb6HGT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, unidentified
• Mutation(s): Yes 


• Deposited: 2018-08-23 Released: 2019-09-04 
• Deposition Author(s): Maw, J., Le Bihan, Y.V., van Montfort, R.L.M.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.280 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 175.01 kDa 
• Atom Count: 11,544 
• Modeled Residue Count: 1,411 
• Deposited Residue Count: 1,500 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A, B, C, D	360	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 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 GTEx:  ENSG00000066135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	E, F, G, H	15	Homo sapiens	Mutation(s): 1  Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA (Subject of Investigation/LOI)	K [auth A], N [auth B], Q [auth C], T [auth D]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
ZN	I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], P [auth C], R [auth D], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OGA	BindingDB:  6HGT	IC50: min: 8.50e+4, max: 2.50e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.280 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.44	α = 90
b = 103.41	β = 99.63
c = 144.52	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Maw, J., Le Bihan, Y.V., van Montfort, R.L.M.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C347/A18364

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description