1NP0

Human lysosomal beta-hexosaminidase isoform B in complex with intermediate analogue NAG-thiazoline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 1NP0

Classification: HYDROLASE

Total Structure Weight: 113472.53

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-hexosaminidase subunit beta A, B 58 Homo sapiens EC#: 3.2.1.52 IUBMB
Fragment: Propeptide residues 50-107
Gene Name(s): HEXB Gene View HCC7
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-hexosaminidase subunit beta chain B C, E 190 Homo sapiens EC#: 3.2.1.52 IUBMB
Fragment: residues 122-311
Gene Name(s): HEXB Gene View HCC7
Beta-hexosaminidase subunit beta chain A D, F 241 Homo sapiens EC#: 3.2.1.52 IUBMB
Fragment: residues 316-556
Gene Name(s): HEXB Gene View HCC7

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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NGT
Query on NGT

A, B 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL- 5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE- 6,7-DIOL
C8 H13 N O4 S
DRHXTSWSUAJOJZ-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NGT Ki: 270000 nM (100) BindingDB

N/A in BindingMoad
Ki: 270000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.198
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 112.41 α = 90.00
b = 112.41 β = 90.00
c = 397.23 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-16
  • Released Date: 2003-04-29
  • Deposition author(s): Mark, B.L., Mahuran, D.J., Cherney, M.M., Zhao, D., Knapp, S., James, M.N.G.

Revision History

  • Version 1_0: 2003-04-29

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Derived calculations, Version format compliance

  • Version 2_0: 2017-08-16

    Type: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary