4HSU

Crystal structure of LSD2-NPAC with H3(1-26)in space group P21

• PDB DOI: https://doi.org/10.2210/pdb4HSU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens, Xenopus laevis
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-30 Released: 2013-02-13 
• Deposition Author(s): Chen, F., Dong, Z., Fang, J., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.232 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

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 - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 104.74 kDa 
• Atom Count: 6,505 
• Modelled Residue Count: 775 
• Deposited Residue Count: 930 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1B	A	776	Homo sapiens	Mutation(s): 0  Gene Names: LSD2 EC: 1
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
Putative oxidoreductase GLYR1	B	124	Homo sapiens	Mutation(s): 0  Gene Names: GLYR1 EC: 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q49A26 (Homo sapiens) Explore Q49A26  Go to UniProtKB:  Q49A26
PHAROS:  Q49A26 GTEx:  ENSG00000140632

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	C	30	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for Q92133 (Xenopus laevis) Explore Q92133  Go to UniProtKB:  Q92133

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ZN	E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.232 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.754	α = 90
b = 89.481	β = 102.89
c = 88.349	γ = 90

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., Dong, Z., Fang, J., 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