4GUS

Crystal structure of LSD2-NPAC with H3 in space group P3221

Structural Biology Knowledgebase: 4GUS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.207

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GUS

Classification: OXIDOREDUCTASE

Total Structure Weight: 104771.63

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
Putative oxidoreductase GLYR1 B 124 Homo sapiens EC#: 1 IUBMB
Fragment: UNP residues 152-268
Gene Name(s): GLYR1 Gene View HIBDL NP60
Histone H3.3 C 21 Homo sapiens Fragment: UNP residues 2-22
Mutation: K4M
Gene Name(s): H3F3A Gene View H3.3A H3F3 PP781 H3F3B Gene View H3.3B

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IOD
Query on IOD

A IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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: 2.23 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.207
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.08 α = 90.00
b = 101.08 β = 90.00
c = 177.37 γ = 120.00

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., Fang, R., Shi, Y., Xu, Y.

Revision History

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