4DO4

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Structural Biology Knowledgebase: 4DO4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.141

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DO4

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 96637.75

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-N-acetylgalactosaminidase A, B 400 Homo sapiens EC#: 3.2.1.49 IUBMB
Fragment: UNP residues 18-411
Mutation: N201Q
Gene Name(s): NAGA Gene View

Small Molecules
Ligands 8 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)
DJN
Query on DJN

A, B N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin- 3-yl]acetamide
DGJNAc, (Synonym)
C8 H16 N2 O4
GBRAQQUMMCVTAV-OSMVPFSASA-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)
BMA
Query on BMA

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-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)
ACY
Query on ACY

A ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DJN N/A in BindingDB
N/A in BindingMoad
Ki: 51 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.141
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 154.05 α = 90.00
b = 114.62 β = 95.82
c = 68.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-09
  • Released Date: 2012-10-10
  • Deposition author(s): Clark, N.E., Garman, S.C.

Revision History

  • 2012-11-21
    Type: Citation | Details: Citation update