SMTL ID : 1np0.3 (2 other biounits)

Human lysosomal beta-hexosaminidase isoform B in complex with intermediate analogue NAG-thiazoline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: M.16, T.17, P.18, L.20 Chain B: N.69 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain D: M.16, T.17, P.18, L.20 Chain E: N.69 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain G: M.16, T.17, P.18, L.20 Chain H: N.69 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain J: M.16, T.17, P.18, L.20 Chain K: N.69 No protein-ligand interaction detected (PLIP)

4 x NGT: 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL(Non-covalent)

NGT.3: 10 residues within 4Å: Chain B: R.90, H.173 Chain C: D.39, E.40, W.90, W.109, Y.135, D.137, W.174, E.176 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:D.39, C:W.90, C:W.109, C:W.174 Hydrogen bonds: C:D.39, C:D.39, C:D.137, B:R.90, B:R.90 NGT.7: 10 residues within 4Å: Chain E: R.90, H.173 Chain F: D.39, E.40, W.90, W.109, Y.135, D.137, W.174, E.176 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:R.90, E:R.90, F:D.39, F:D.39, F:D.137 Hydrophobic interactions: F:W.90, F:W.109, F:W.174 NGT.11: 10 residues within 4Å: Chain H: R.90, H.173 Chain I: D.39, E.40, W.90, W.109, Y.135, D.137, W.174, E.176 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: I:D.39, I:W.90, I:W.109, I:W.174 Hydrogen bonds: I:D.39, I:D.137, H:R.90, H:R.90 NGT.15: 10 residues within 4Å: Chain K: R.90, H.173 Chain L: D.39, E.40, W.90, W.109, Y.135, D.137, W.174, E.176 7 PLIP interactions: 5 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:W.90, L:W.109, L:W.174 Hydrogen bonds: L:D.39, L:D.137, K:R.90, K:R.90

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: T.11, S.27, T.29, K.40, A.41, N.42 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.11, B:T.11, B:S.27, B:N.42 GOL.5: 10 residues within 4Å: Chain C: G.142, Q.143, D.144, W.145, P.189, R.190, Q.229, P.230, L.231 Chain I: Y.177 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.144, C:W.145, C:Q.229, C:Q.229, C:L.231 GOL.8: 9 residues within 4Å: Chain F: G.142, Q.143, D.144, W.145, P.189, R.190, Q.229, P.230, L.231 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.142, F:D.144, F:D.144, F:W.145, F:Q.229, F:Q.229, F:L.231 GOL.12: 6 residues within 4Å: Chain H: T.11, S.27, T.29, K.40, A.41, N.42 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:T.11, H:S.27, H:N.42 GOL.13: 10 residues within 4Å: Chain C: Y.177 Chain I: G.142, Q.143, D.144, W.145, P.189, R.190, Q.229, P.230, L.231 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:D.144, I:D.144, I:W.145, I:Q.229, I:Q.229, I:L.231 GOL.16: 9 residues within 4Å: Chain L: G.142, Q.143, D.144, W.145, P.189, R.190, Q.229, P.230, L.231 6 PLIP interactions: 6 interactions with chain L Hydrogen bonds: L:G.142, L:D.144, L:W.145, L:Q.229, L:Q.229, L:L.231

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain F: R.57, Q.58 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.58 Water bridges: F:R.57, F:R.57, F:R.57 Salt bridges: F:R.57 SO4.14: 2 residues within 4Å: Chain L: R.57, Q.58 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:Q.58 Water bridges: L:R.57, L:R.57, L:R.57 Salt bridges: L:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mark, B.L. et al., Crystal structure of Human beta-hexosaminidase B: Understanding the molecular basis of Sandhoff and Tay-Sachs disease. J.Mol.Biol. (2003)

Release Date

2003-04-29

Peptides

Beta-hexosaminidase subunit beta: ADGJ
Beta-hexosaminidase subunit beta chain B: BEHK
Beta-hexosaminidase subunit beta chain A: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
A

J
B

B
C

E
E

H
C

K
E

C
D

F
F

I
D

L
F

Beta-hexosaminidase subunit beta

Beta-hexosaminidase subunit beta chain B

Beta-hexosaminidase subunit beta chain A

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