Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 129124.64 
• Atom Count: 7926 
• Residue Count: 1112 
• Unique protein chains: 1

3LMY

The Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine

• DOI: 10.2210/pdb3LMY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens


• Deposited: 2010-02-01 Released: 2011-02-16 
• Deposition Author(s): Bateman, K.S., Cherney, M.M., Withers, S.G., Mahuran, D.J., Tropak, M., James, M.N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.252 
• R-Value Work: 0.194 

Literature

The Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine

Bateman, K.S., Cherney, M.M., Withers, S.G., Mahuran, D.J., Tropak, M., James, M.N.G.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Beta-hexosaminidase subunit beta	A, B	556	Homo sapiens	Mutation(s): 0  Gene Names: HEXB EC: 3.2.1.52
Find proteins for P07686 (Homo sapiens) Go to Gene View: HEXB Go to UniProtKB:  P07686

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NDG	A, B	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
CP6	A, B	5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE PYRIMETHAMINE C12 H13 Cl N4 WKSAUQYGYAYLPV-UHFFFAOYSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CP6	IC50: 4500 - 9100 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.252 
• R-Value Work: 0.194 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 113.898	α = 90.00
b = 113.898	β = 90.00
c = 397.427	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
Blu-Ice	data collection
CCP4	phasing
REFMAC	refinement
CCP4	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-01 
• Released Date: 2011-02-16 
• Deposition Author(s): Bateman, K.S., Cherney, M.M., Withers, S.G., Mahuran, D.J., Tropak, M., James, M.N.G.

Revision History 

• Version 1.0: 2011-02-16
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance