5A7W

Crystal structure of human JMJD2A in complex with compound 35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 5A7W

Classification: OXIDOREDUCTASE

Total Structure Weight: 90253.61

Macromolecule Entities
Molecule Chains Length Organism Details
LYSINE-SPECIFIC DEMETHYLASE 4A A 381 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: RESIDUES 1-359
Gene Name(s): KDM4A Gene View JHDM3A JMJD2 JMJD2A KIAA0677
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
LYSINE-SPECIFIC DEMETHYLASE 4A B 381 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: RESIDUES 1-359
Mutation: Q232E
Gene Name(s): KDM4A Gene View JHDM3A JMJD2 JMJD2A KIAA0677

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
35M
Query on 35M

A, B 2-[5-[(4-hydroxyphenyl)carbonylamino]-2-oxidanyl- phenyl]pyridine-4-carboxylic acid
C19 H14 N2 O5
MXKVATSZRALAIN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.225
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 101.24 α = 90.00
b = 149.75 β = 90.00
c = 57.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-07-10
  • Released Date: 2016-01-13
  • Deposition author(s): Nowak, R., Velupillai, S., Krojer, T., Gileadi, C., Johansson, C., Korczynska, M., Le, D.D., Younger, N., Gregori-Puigjane, E., Tumber, A., Iwasa, E., Pollock, S.B., Ortiz Torres, I., Kopec, J., Tallant, C., Froese, S., Von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Shoichet, B.K., Fujimori, D.G., Oppermann, U.

Revision History

  • Version 1_0: 2016-01-13

    Type: Initial release

  • Version 1_1: 2016-03-09

    Type: Database references