5FZD

Crystal structure of the catalytic domain of human JARID1B in complex with L-2-hydroxyglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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 L-2-Hydroxyglutarate

Nowak, R.Kopec, J.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
A
479Homo sapiensMutation(s): 0 
Gene Names: KDM5BJARID1BPLU1RBBP2H1
EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for Q9UGL1 (Homo sapiens)
Go to UniProtKB:  Q9UGL1
NIH Common Fund Data Resources
PHAROS  Q9UGL1
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
S2G
Query on S2G

Download CCD File 
A
(2S)-2-HYDROXYPENTANEDIOIC ACID
C5 H8 O5
HWXBTNAVRSUOJR-VKHMYHEASA-N
 Ligand Interaction
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
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
MN
Query on MN

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

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.8α = 90
b = 141.8β = 90
c = 151.41γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
DIMPLEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references, Structure summary