9F0A | pdb_00009f0a

N5 Adduct of LSD1-CoREST in complex with MC4455

• PDB DOI: https://doi.org/10.2210/pdb9F0A/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-15 Released: 2025-04-23 
• Deposition Author(s): Barone, M., Mattevi, A.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.36 Å
• R-Value Free: 
  0.234 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

N5 Adduct of LSD1-CoREST in complex with MC4455

Barone, M., Mattevi, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 102.77 kDa 
• Atom Count: 6,380 
• Modeled Residue Count: 799 
• Deposited Residue Count: 908 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1A	A	730	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
PHAROS:  O60341 GTEx:  ENSG00000004487

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REST corepressor 1	B	178	Homo sapiens	Mutation(s): 0  Gene Names: RCOR1, KIAA0071, RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0  Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0 GTEx:  ENSG00000089902

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H8N (Subject of Investigation/LOI)	C [auth A]	[[(2~{S},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{R})-5-[5-[3-[4-[[4-[[(2~{S})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]carbamoyl]pyridin-2-yl]amino]phenyl]propanoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a}~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate C54 H63 N13 O18 P2 XWHWYVHMOOWMKZ-MBYMQWEBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.36 Å
• R-Value Free:  0.234 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.438	α = 90
b = 179.767	β = 90
c = 234.461	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Barone, M., Mattevi, A.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	MUR project 404 FISR2019_00374 MeDyCa

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release