4FWF

Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic

Structural Biology Knowledgebase: 4FWF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FWF

Classification: OXIDOREDUCTASE / PROTEIN BINDING

Total Structure Weight: 92516.00

Macromolecule Entities
Molecule Chains Length Organism Details
Lysine-specific histone demethylase 1B A 796 Homo sapiens EC#: 1 IUBMB
Fragment: UNP residues 30-822
Gene Name(s): KDM1B Gene View AOF1 C6orf193 LSD2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H3.1 E 20 Homo sapiens Fragment: UNP residues 2-21
Mutation: K4M
Gene Name(s): HIST1H3A Gene View H3FA HIST1H3B Gene View H3FL HIST1H3C Gene View H3FC HIST1H3D Gene View H3FB HIST1H3E Gene View H3FD HIST1H3F Gene View H3FI HIST1H3G Gene View H3FH HIST1H3H Gene View H3FK HIST1H3I Gene View H3FF HIST1H3J Gene View H3FJ
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 FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.206
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.44 α = 90.00
b = 98.54 β = 96.08
c = 101.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-01
  • Released Date: 2013-01-16
  • Deposition author(s): Zhang, Q., Chen, Z.

Revision History

  • 2013-07-03
    Type: Citation | Details: Citation update