5FYB

Crystal structure of the catalytic domain of human JARID1B in complex with MC1648


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc1648

Nowak, R.Srikannathasan, V.Rotili, D.Johansson, C.Gileadi, C.Kupinska, K.Strain-Damerell, C.Szykowska, A.von Delft, F.Burgess-Brown, N.A.Arrowsmith, C.H.Bountra, C.Edwards, A.M.Oppermann, U.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B
A
479Homo sapiensMutation(s): 0 
Gene Names: KDM5B (JARID1B, PLU1, RBBP2H1)
EC: 1.14.11.-
Find proteins for Q9UGL1 (Homo sapiens)
Go to Gene View: KDM5B
Go to UniProtKB:  Q9UGL1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 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
77J
Query on 77J

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Download CCD File 
A
N-hydroxy-3-[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]propanamide
C13 H13 N3 O3 S
WNPFBIDOQFZHQF-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 142.110α = 90.00
b = 142.110β = 90.00
c = 151.670γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
DIMPLEphasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references, Structure summary