3LMY

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase subunit beta
A, B
556Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
CP6
Query on CP6

Download SDF File 
Download CCD File 
A, B
5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
PYRIMETHAMINE
C12 H13 Cl N4
WKSAUQYGYAYLPV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CP6IC50: 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 = 113.898α = 90.00
b = 113.898β = 90.00
c = 397.427γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
Blu-Icedata collection
CCP4phasing
REFMACrefinement
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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