5FYI

Crystal structure of human JMJD2A in complex with pyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 5FYI

Classification: OXIDOREDUCTASE

Total Structure Weight: 90568.52

Macromolecule Entities
Molecule Chains Length Organism Details
LYSINE-SPECIFIC DEMETHYLASE 4A A, B 381 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: RESIDUES 4-354
Gene Name(s): KDM4A Gene View JHDM3A JMJD2 JMJD2A KIAA0677
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1KA
Query on 1KA

B (2-hydroxyethoxy)acetaldehyde
C4 H8 O3
DSGGHBUAHUMMHN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PYR
Query on PYR

A, B PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A, B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.197
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 100.45 α = 90.00
b = 148.83 β = 90.00
c = 57.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-03-07
  • Released Date: 2016-03-16
  • Deposition author(s): Nowak, R., Kopec, J., Johansson, C., Szykowska, A., Von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Revision History

  • Version 1_0: 2016-03-16

    Type: Initial release