2IW5

Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 2IW5

Classification: OXIDOREDUCTASE / TRANSCRIPTION REGULATOR

Total Structure Weight: 101646.65

Macromolecule Entities
Molecule Chains Length Organism Details
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 A 666 Homo sapiens EC#: 1 IUBMB
Fragment: SWIRM DOMAIN, AMINE OXIDASE DOMAIN AND LINKER, RESIDUES 171-836
Gene Name(s): KDM1A Gene View AOF2 KDM1 KIAA0601 LSD1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
REST COREPRESSOR 1 B 235 Homo sapiens Fragment: FRAGMENT OF SANT1, LINKER REGION AND SANT2 DOMAIN, RESIDUES 286-482
Gene Name(s): RCOR1 Gene View KIAA0071 RCOR
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

A FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NH4
Query on NH4

A AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.203
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 120.35 α = 90.00
b = 178.22 β = 90.00
c = 234.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-26
  • Released Date: 2006-08-09
  • Deposition author(s): Yang, M., Gocke, C.B., Luo, X., Borek, D., Tomchick, D.R., Machius, M., Otwinowski, Z., Yu, H.

Revision History

  • 2011-07-13
    Type: Advisory, Version format compliance