6H10

Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR073


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.121 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR073

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

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: KDM4DJHDM3DJMJD2D
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
Find proteins for Q6B0I6 (Homo sapiens)
Go to UniProtKB:  Q6B0I6
NIH Common Fund Data Resources
PHAROS  Q6B0I6
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FJ8
Query on FJ8

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A
~{N}-[(~{E})-(4-methylphenyl)methylideneamino]-2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanamide
C11 H12 N6 O
CVRGHXWTBXFGAR-KPKJPENVSA-N
 Ligand Interaction
EPE
Query on EPE

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A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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

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A
1,2-ETHANEDIOL
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
CL
Query on CL

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

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.121 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.454α = 90
b = 71.454β = 90
c = 150.693γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-29
    Type: Initial release