4DO5

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Structural Biology Knowledgebase: 4DO5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DO5

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 96279.40

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 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BMA
Query on BMA

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
JSmol
CIT
Query on CIT

A, B CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
DGJ
Query on DGJ

A, B (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine- 3,4,5-triol
1-deoxygalactonojirimycin (Synonym)
C6 H13 N O4
LXBIFEVIBLOUGU-DPYQTVNSSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A, B GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MAN
Query on MAN

A, B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
JSmol
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DGJ N/A in BindingDB
N/A in BindingMoad
Ki: 1480 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.159
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 154.35 α = 90.00
b = 114.51 β = 95.64
c = 68.55 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