4FDI

The molecular basis of mucopolysaccharidosis IV A

Structural Biology Knowledgebase: 4FDI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FDI

Classification: HYDROLASE

Total Structure Weight: 114137.65

Macromolecule Entities
Molecule Chains Length Organism Details
N-acetylgalactosamine-6-sulfatase A, B 502 Homo sapiens EC#: 3.1.6.4 IUBMB
Fragment: UNP residues 27-522
Gene Name(s): GALNS Gene View

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

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

A, B CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
DDZ
Query on DDZ
A, B L-PEPTIDE LINKING C3 H7 N O4 ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.164
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.37 α = 90.00
b = 155.52 β = 113.76
c = 62.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-28
  • Released Date: 2012-09-05
  • Deposition author(s): Rivera-Colon, Y., Garman, S.C.

Revision History

  • 2012-10-31
    Type: Citation | Details: Citation update
  • 2012-09-19
    Type: Citation | Details: Citation update