6ETT

Crystal structure of KDM4D with tetrazole compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.257 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of KDM4D with tetrazolylhydrazide ligand NR016

Malecki, P.H.Weiss, M.S.Heinemann, U.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4D
A
342Homo 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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BXH
Query on BXH

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A
ethyl 2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoate
C5 H8 N4 O2
NAOHMNNTUFFTBF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-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: 1.257 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.123 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.450α = 90.00
b = 71.450β = 90.00
c = 150.539γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release