8UNI | pdb_00008uni

LSD1-CoREST with N-formyl-FAD in complex with H3K4M histone tail

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.252 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HUFClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history. 


Literature

Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1

Caroli, J., Mattevi, A.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific histone demethylase 1A871Homo sapiensMutation(s): 0 
Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1
EC: 1.14.99.66
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens)
Explore O60341 
Go to UniProtKB:  O60341
PHAROS:  O60341
GTEx:  ENSG00000004487 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60341
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
REST corepressor 1144Homo sapiensMutation(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 Groups  
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UniProt GroupQ9UKL0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3 (Fragment)21Homo sapiensMutation(s): 1 
UniProt
Find proteins for V9H1G0 (Homo sapiens)
Explore V9H1G0 
Go to UniProtKB:  V9H1G0
Entity Groups  
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UniProt GroupV9H1G0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HUF (Subject of Investigation/LOI)
Query on HUF
Download Ideal Coordinates CCD File 
D [auth A][[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate
C28 H35 N9 O16 P2
KZQASMOVHMAAKH-MZWSMYJRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.252 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.782α = 90
b = 178.172β = 90
c = 234.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HUFClick on this verticalbar to view details

View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG19808

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release