4GUT

Crystal structure of LSD2-NPAC

Structural Biology Knowledgebase: 4GUT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GUT

Classification: OXIDOREDUCTASE

Total Structure Weight: 101896.66

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

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
 
JSmol
GOL
Query on GOL

A GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
PGE
Query on PGE

B TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.196
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.00 α = 90.00
b = 89.76 β = 104.96
c = 86.69 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., Fang, R., Shi, Y., Xu, Y.

Revision History

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