4GU0

Crystal structure of LSD2 with H3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.103 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into substrate recognition by histone demethylase LSD2/KDM1b

Chen, F.Yang, H.Dong, Z.Fang, J.Wang, P.Zhu, T.Gong, W.Fang, R.Shi, Y.G.Li, Z.Xu, Y.

(2013) Cell Res. 23: 306-309


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific histone demethylase 1B
A, B, C, D
776Homo sapiensMutation(s): 0 
Gene Names: KDM1B (AOF1, C6orf193, LSD2)
EC: 1.-.-.-
Find proteins for Q8NB78 (Homo sapiens)
Go to Gene View: KDM1B
Go to UniProtKB:  Q8NB78
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
E, F
26Homo sapiensMutation(s): 1 
Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens)
Go to Gene View: H3F3A H3F3B
Go to UniProtKB:  P84243
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.103 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 101.843α = 94.47
b = 108.926β = 112.34
c = 120.825γ = 117.95
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references