5FYC

Crystal structure of human JMJD2A in complex with succinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.261 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Human Jmjd2A in Complex with Succinate

Nowak, R.Kopec, J.Johansson, C.Szykowska, A.von Delft, F.Arrowsmith, C.H.Bountra, C.Edwards, A.Oppermann, U.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC DEMETHYLASE 4A
A, B
381Homo sapiensMutation(s): 0 
Gene Names: KDM4A (JHDM3A, JMJD2, JMJD2A, KIAA0677)
EC: 1.14.11.-
Find proteins for O75164 (Homo sapiens)
Go to Gene View: KDM4A
Go to UniProtKB:  O75164
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
FUM
Query on FUM

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A, B
FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.261 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.650α = 90.00
b = 149.440β = 90.00
c = 57.280γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
DIMPLEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references, Structure summary