6H8P

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.983 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26.

Walport, L.J.Hopkinson, R.J.Chowdhury, R.Zhang, Y.Bonnici, J.Schiller, R.Kawamura, A.Schofield, C.J.

(2018) FEBS Lett. 592: 3264-3273


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4A
A, B
381Homo sapiensMutation(s): 0 
Gene Names: KDM4A (JHDM3A, JMJD2, JMJD2A, KIAA0677)
EC: 1.14.11.-
Find proteins for O75164 (Homo sapiens)
Go to Gene View: KDM4A
Go to UniProtKB:  O75164
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H1.4
C, D
15Homo sapiensMutation(s): 0 
Gene Names: HIST1H1E (H1F4)
Find proteins for P10412 (Homo sapiens)
Go to Gene View: HIST1H1E
Go to UniProtKB:  P10412
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

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Download CCD File 
A, B
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
C, D
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.983 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.722α = 90.00
b = 150.146β = 90.00
c = 57.601γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Database references