6EK6

Crystal structure of KDM5B in complex with S49195a.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of KDM5B in complex with S49195a.

Srikannathasan, V.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
A
455Homo 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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 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
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
90V
Query on 90V

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A
N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide
C15 H22 N4 O2
CXEXTVGTDZRKJS-LLVKDONJSA-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: 2.05 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 141.410α = 90.00
b = 141.410β = 90.00
c = 150.950γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release