4GU0

Crystal structure of LSD2 with H3

Structural Biology Knowledgebase: 4GU0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 4GU0

Classification: OXIDOREDUCTASE

Total Structure Weight: 357722.41

Macromolecule Entities
Molecule Chains Length Organism Details
Lysine-specific histone demethylase 1B A, B, C, D 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
Histone H3.3 E, F 26 Homo sapiens Fragment: UNP residues 2-27
Mutation: K4M
Gene Name(s): H3F3A Gene View H3.3A H3F3 PP781 H3F3B Gene View H3.3B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

A, B, C, D 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: 3.1 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.204
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.84 α = 94.47
b = 108.93 β = 112.34
c = 120.82 γ = 117.95

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-29
  • Released Date: 2013-02-13
  • Deposition author(s): Chen, F., Yang, H., Dong, Z., Fang, J., Zhu, T., Gong, W., Xu, Y.

Revision History

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