Macromolecules
Sequence Display for 2GK1

Classification: HYDROLASE

Total Structure Weight: 455847.94

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-hexosaminidase subunit alpha A, C, E, G 52 Homo sapiens EC#: 3.2.1.52 IUBMB
Fragment: Propeptide residues 23-74
Gene Name(s): HEXA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-hexosaminidase subunit alpha I, J, K, L 440 Homo sapiens EC#: 3.2.1.52 IUBMB
Fragment: residues 89-528
Mutation: I436V
Gene Name(s): HEXA Gene View
Beta-hexosaminidase subunit beta B, D, F, H 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 M, O, Q, S 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 N, P, R, T 237 Homo sapiens EC#: 3.2.1.52 IUBMB
Fragment: residues 316-552
Gene Name(s): HEXB Gene View HCC7

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

A, B, C, D, E, F, G, H 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, C, D, E, F, G, H 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)
BMA
Query on BMA

A, B, C, G BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.322
  • R-Value Work: 0.274
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 322.25 α = 90.00
b = 109.80 β = 91.48
c = 132.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-31
  • Released Date: 2006-05-30
  • Deposition author(s): Lemieux, M.J., Mark, B.L., Cherney, M.M., Withers, S.G., Mahuran, D.J., James, M.N.

Revision History

  • Version 1_0: 2006-05-30

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 2_0: 2017-08-16

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

  • Version 2_1: 2017-10-18

    Type: Refinement description