4GUU

Crystal structure of LSD2-NPAC with tranylcypromine

Structural Biology Knowledgebase: 4GUU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.199

Literature

Macromolecules
Sequence Display for 4GUU

Classification: OXIDOREDUCTASE

Total Structure Weight: 101696.51

Macromolecule Entities
Molecule Chains Length Organism Details
Lysine-specific histone demethylase 1B A 776 Homo sapiens EC#: 1 IUBMB
Fragment: UNP residues 51-822
Gene Name(s): KDM1B Gene View AOF1 C6orf193 LSD2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Putative oxidoreductase GLYR1 B 124 Homo sapiens EC#: 1 IUBMB
Fragment: UNP residues 152-268
Gene Name(s): GLYR1 Gene View HIBDL NP60
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FA9
Query on FA9

A [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)- 3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)- 5-[(3R,3aS,7aR)-10,11-dimethyl-1,4,6-trioxo- 3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1- e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate
C36 H43 N9 O16 P2
QWOOVYWBGZGGNV-ITRBMUPBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.199
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 62.82 α = 90.00
b = 90.16 β = 104.20
c = 87.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-29
  • Released Date: 2013-01-16
  • Deposition author(s): Chen, F., Dong, Z., Fang, J., Yang, Y., Li, Z., Xu, Y., Yang, H., Wang, P., Xu, Y.

Revision History

  • 2013-07-10
    Type: Citation | Details: Citation update