3LMY

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

• PDB DOI: https://doi.org/10.2210/pdb3LMY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• 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: 2.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

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.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 129.07 kDa 
• Atom Count: 8,004 
• Modelled Residue Count: 959 
• Deposited Residue Count: 1,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hexosaminidase subunit beta	A, B	556	Homo sapiens	Mutation(s): 0  EC: 3.2.1.52
UniProt & NIH Common Fund Data Resources
Find proteins for P07686 (Homo sapiens) Explore P07686  Go to UniProtKB:  P07686
PHAROS:  P07686 GTEx:  ENSG00000049860

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CP6	G [auth A], L [auth B]	5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE C12 H13 Cl N4 WKSAUQYGYAYLPV-UHFFFAOYSA-N
NAG	F [auth A], H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NDG	E [auth A], J [auth B]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
SO4	K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
CP6	BindingDB:  3LMY	IC50: min: 4500, max: 1.50e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.898	α = 90
b = 113.898	β = 90
c = 397.427	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary