4UXN | pdb_00004uxn

LSD1(KDM1A)-CoREST in complex with Z-Pro derivative of MC2580

• PDB DOI: https://doi.org/10.2210/pdb4UXN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-08-27 Released: 2015-02-25 
• Deposition Author(s): Rodriguez, V., Valente, S., Stazi, G., Lucidi, A., Mercurio, C., Vianello, P., Ciossani, G., Mattevi, A., Botrugno, O.A., Dessanti, P., Minucci, S., Varasi, M., Mai, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Pyrrole- and Indole-Containing Tranylcypromine Derivatives as Novel Lysine-Specific Demethylase 1 Inhibitors Active on Cancer Cells

Rodriguez, V., Valente, S., Rovida, S., Rotili, D., Stazi, G., Lucidi, A., Ciossani, G., Mattevi, A., Botrugno, O.A., Dessanti, P., Mercurio, C., Vianello, P., Minucci, S., Varasi, M., Mai, A.

(2015) ChemMedChem 6: 665-670

• DOI: https://doi.org/10.1039/C4MD00507D

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 147.28 kDa 
• Atom Count: 6,374 
• Modelled Residue Count: 799 
• Deposited Residue Count: 1,334 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A	A	852	Homo sapiens	Mutation(s): 0  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	482	Homo sapiens	Mutation(s): 0
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
M8A	D [auth A]	benzyl (2R)-2-{[4-(3-oxopropyl)phenyl]carbamoyl}pyrrolidine-1-carboxylate C22 H24 N2 O4 ACUUWDZYZLDIFD-HXUWFJFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.98	α = 90
b = 177.76	β = 90
c = 233.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Rodriguez, V., Valente, S., Stazi, G., Lucidi, A., Mercurio, C., Vianello, P., Ciossani, G., Mattevi, A., Botrugno, O.A., Dessanti, P., Minucci, S., Varasi, M., Mai, A.

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references
• Version 1.2: 2018-06-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description