1P0Y

Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy

Structural Biology Knowledgebase: 1P0Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.228

Literature

Macromolecules
Sequence Display for 1P0Y

Classification: TRANSFERASE

Total Structure Weight: 153202.72

Macromolecule Entities
Molecule Chains Length Organism Details
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast A, B, C 444 Pisum sativum EC#: 2.1.1.127 IUBMB
Gene Name(s): RBCMT
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MLZ
Query on MLZ

C N-METHYL-LYSINE
C7 H16 N2 O2
PQNASZJZHFPQLE-LURJTMIESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MLZ N/A in BindingDB
N/A in BindingMoad
Ki: 100800000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.228
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 130.41 α = 90.00
b = 153.19 β = 90.00
c = 266.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-11
  • Released Date: 2003-07-01
  • Deposition author(s): Trievel, R.C., Flynn, E.M., Houtz, R.L., Hurley, J.H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4