5PHF

PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09688a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.389 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Pearce, N.M.Krojer, T.Bradley, A.R.Collins, P.Nowak, R.P.Talon, R.Marsden, B.D.Kelm, S.Shi, J.Deane, C.M.von Delft, F.

(2017) Nat Commun 8: 15123-15123


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4D
A
364Homo sapiensMutation(s): 0 
Gene Names: KDM4D (JHDM3D, JMJD2D)
EC: 1.14.11.-
Find proteins for Q6B0I6 (Homo sapiens)
Go to Gene View: KDM4D
Go to UniProtKB:  Q6B0I6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

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A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
URS
Query on URS

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A
N-PHENYLTHIOUREA
C7 H8 N2 S
FULZLIGZKMKICU-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.389 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.129 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.629α = 90.00
b = 71.629β = 90.00
c = 150.584γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2017-10-04
    Type: Structure summary