12LQ | pdb_000012lq

LSD1-CoREST in complex with Alkyne probe and peptide PRCALVKSK

• PDB DOI: https://doi.org/10.2210/pdb12LQ/pdb

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


• Deposited: 2026-04-12 Released: 2026-11-11 
• Deposition Author(s): Caroli, J., Mattevi, A.
• Funding Organization(s): Italian Association for Cancer Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Covalent Chemical Rescue of a Transcription Factor-Corepressor Complex

Liu, C., Yost, K., Kwok, H.S., Caroli, J., Waterbury, A.L., Gankhuyag, N., Zhang, O., Harry, S.A., Hansen, T.N., Roh, H., Furui, A., Mattevi, A., Liau, B.B.

(2026) ACS Cent Sci 

• DOI: https://doi.org/10.1021/acscentsci.6c01320

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 113.25 kDa 
• Atom Count: 6,410 
• Modeled Residue Count: 806 
• Deposited Residue Count: 1,022 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1A	A	871	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1.14.99.66 (PDB Primary Data), 1.14.11 (UniProt), 1.14.11.65 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
GTEx:  ENSG00000004487

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REST corepressor 1	B	144	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide PRCALVKSK	C	7	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1DCL (Subject of Investigation/LOI)	D [auth C]	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(2-ethyl-1,3-thiazol-4-yl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) C35 H44 N10 O16 P2 S FRWDRNSIFBXXQK-ILLVBOIVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.869	α = 90
b = 180.49	β = 90
c = 234.517	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-11 
Deposition Author(s): Caroli, J., Mattevi, A.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	IG19808

Revision History  

• Version 1.0: 2026-11-11
  Type: Initial release