1YDH

X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.159

Literature

Macromolecules
Sequence Display for 1YDH

Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION

Total Structure Weight: 48788.77

Macromolecule Entities
Molecule Chains Length Organism Details
At5g11950 A, B 216 Arabidopsis thaliana EC#: 3.2.2.n1 IUBMB
Mutation: M54M, M77M, M95M, M102M, M119M, M125M, M181M, M184M, M192M
Gene Name(s): LOG8 At5g11950 F14F18.120
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.159
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 121.59 α = 90.00
b = 80.43 β = 102.97
c = 50.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-23
  • Released Date: 2005-01-11
  • Deposition author(s): Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance