3LMY

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

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 

wwPDB Validation 3D Report Full Report



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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit betaA, B556Homo sapiensMutation(s): 0 
Gene Names: HEXB, HCC7
EC: 3.2.1.52
Find proteins for P07686 (Homo sapiens)
Explore P07686 
Go to UniProtKB:  P07686
NIH Common Fund Data Resources
PHAROS  P07686
GTEx  ENSG00000049860
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
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
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2 N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CP6
Query on CP6
Download CCD File 
A, B
5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
C12 H13 Cl N4
WKSAUQYGYAYLPV-UHFFFAOYSA-N		 Ligand Interaction
NDG
Query on NDG
Download CCD File 
A, B
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N		 Ligand Interaction
NAG
Query on NAG
Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
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 = 113.898α = 90
b = 113.898β = 90
c = 397.427γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

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