1N2K

Crystal structure of a covalent intermediate of endogenous human arylsulfatase A

Structural Biology Knowledgebase: 1N2K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 1N2K

Classification: HYDROLASE

Total Structure Weight: 52725.00

Macromolecule Entities
Molecule Chains Length Organism Details
ARYLSULFATASE A A 489 Homo sapiens EC#: 3.1.6.8 IUBMB
Mutation: C69X
Gene Name(s): ARSA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FGP
Query on FGP
A L-PEPTIDE LINKING C3 H8 N O7 P SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.202
  • Space Group: I 4 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 131.52 α = 90.00
b = 131.52 β = 90.00
c = 192.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-23
  • Released Date: 2003-12-23
  • Deposition author(s): Chruszcz, M., Laidler, P., Monkiewicz, M., Ortlund, E., Lebioda, L., Lewinski, K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update