1JG3

Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate

Structural Biology Knowledgebase: 1JG3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 1JG3

Classification: TRANSFERASE

Total Structure Weight: 55281.48

Macromolecule Entities
Molecule Chains Length Organism Details
protein-L-isoaspartate O-methyltransferase A, B 235 Pyrococcus furiosus EC#: 2.1.1.77 IUBMB
Gene Name(s): pcm PF1922
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
VYP(L-iso-ASP)HA C, D 6 synthetic Details: hexapeptide substrate

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

A, B ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
IAS
Query on IAS
C, D L-beta-peptide, C-gamma linking C4 H7 N O4 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.204
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.57 α = 90.00
b = 91.57 β = 90.00
c = 124.55 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-06-22
  • Released Date: 2001-11-16
  • Deposition author(s): Griffith, S.C., Sawaya, M.R., Boutz, D., Thapar, N., Katz, J., Clarke, S., Yeates, T.O.

Revision History

  • 2011-07-27
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-27
    Type: Linkage | Details: Linkage
  • 2011-07-27
    Type: Sequence database correspondence | Details: Changed residue name in the sequence
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4