SMTL ID : 3lmy.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: M.65, T.66, P.67, L.69, N.190 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain B: M.65, T.66, P.67, L.69, N.190 No protein-ligand interaction detected (PLIP)

2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Post Translational Modification)

NDG.2: 4 residues within 4Å: Chain A: E.136, N.142, S.144, Q.347 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.347 Hydrogen bonds: A:N.142 Water bridges: A:E.136, A:S.145 NDG.6: 4 residues within 4Å: Chain B: E.136, N.142, S.144, Q.347 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.347 Hydrogen bonds: B:N.142 Water bridges: B:E.136, B:S.145

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.327 NAG.7: 1 residues within 4Å: Chain B: N.327 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.327

2 x CP6: 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE(Non-covalent)

CP6.4: 13 residues within 4Å: Chain A: R.211, H.237, D.240, D.290, H.294, D.354, E.355, W.424, Y.450, D.452, L.453, W.489, E.491 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:D.354, A:W.424, A:W.424, A:W.489 Hydrogen bonds: A:R.211, A:R.211, A:D.290, A:D.290, A:E.491 Salt bridges: A:D.240, A:D.354, A:E.355 pi-Stacking: A:Y.450, A:W.489 pi-Cation interactions: A:H.294, A:W.489 CP6.8: 13 residues within 4Å: Chain B: R.211, H.237, D.240, D.290, H.294, D.354, E.355, W.424, Y.450, D.452, L.453, W.489, E.491 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:D.354, B:W.424, B:W.424, B:W.489 Hydrogen bonds: B:R.211, B:R.211, B:D.290, B:E.491 Salt bridges: B:D.240, B:D.354, B:E.355 pi-Stacking: B:Y.450, B:W.489 pi-Cation interactions: B:H.294, B:W.489

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bateman, K.S. et al., The Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine. To be Published

Release Date

2011-02-16

Peptides

Beta-hexosaminidase subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-hexosaminidase subunit beta

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