4GU0

Crystal structure of LSD2 with H3

• PDB DOI: https://doi.org/10.2210/pdb4GU0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-08-29 Released: 2013-02-13 
• Deposition Author(s): Chen, F., Yang, H., Dong, Z., Fang, J., Zhu, T., Gong, W., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.221 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Starting Model: experimental

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

• PubMed: 23357850 
• DOI: https://doi.org/10.1038/cr.2013.17
• Primary Citation of Related Structures:  
  4GU0, 4HSU

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 357.72 kDa 
• Atom Count: 24,156 
• Modelled Residue Count: 3,019 
• Deposited Residue Count: 3,156 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1B	A, B, C, D	776	Homo sapiens	Mutation(s): 0  Gene Names: LSD2 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB78 (Homo sapiens) Explore Q8NB78  Go to UniProtKB:  Q8NB78
PHAROS:  Q8NB78 GTEx:  ENSG00000165097

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	E, F	26	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243 GTEx:  ENSG00000132475 ENSG00000163041

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	G [auth A], K [auth B], O [auth C], S [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ZN	H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], P [auth C], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.221 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.843	α = 94.47
b = 108.926	β = 112.34
c = 120.825	γ = 117.95

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Chen, F., Yang, H., Dong, Z., Fang, J., Zhu, T., Gong, W., Xu, Y.

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description