SMTL ID : 1now.1 (1 other biounit)

Human lysosomal beta-hexosaminidase isoform B in complex with (2R,3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (GalNAc-isofagomine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 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, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: M.16, T.17, P.18, L.20, N.141 No protein-ligand interaction detected (PLIP)

2 x IFG: (2R,3R,4S,5R)-2-ACETAMIDO-3,4-DIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE(Non-covalent)

IFG.2: 11 residues within 4Å: Chain A: R.162, H.245, D.305, E.306, W.356, W.375, Y.401, D.403, W.440, E.442 Chain B: Y.407 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.305, A:W.356, A:W.375, A:W.440, A:W.440 Hydrogen bonds: A:R.162, A:R.162, A:H.245, A:D.305, A:D.305, B:Y.407 Water bridges: A:D.403 IFG.6: 11 residues within 4Å: Chain A: Y.407 Chain B: R.162, H.245, D.305, E.306, W.356, W.375, Y.401, D.403, W.440, E.442 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:Y.407, B:R.162, B:R.162, B:H.245, B:D.305, B:Y.401 Hydrophobic interactions: B:D.305, B:W.356, B:W.375, B:W.440, B:W.440

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.99, Y.100, T.101, K.112, A.113, N.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.83, A:T.83, A:S.99, A:N.114 Water bridges: A:K.112 GOL.4: 10 residues within 4Å: Chain A: G.408, Q.409, D.410, W.411, P.455, R.456, Q.495, P.496, L.497 Chain B: Y.443 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.410, A:W.411, A:Q.495, A:Q.495, A:L.497 GOL.7: 6 residues within 4Å: Chain B: S.99, Y.100, T.101, K.112, A.113, N.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.83, B:S.99, B:N.114 Water bridges: B:K.112 GOL.8: 10 residues within 4Å: Chain A: Y.443 Chain B: G.408, Q.409, D.410, W.411, P.455, R.456, Q.495, P.496, L.497 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.410, B:D.410, B:W.411, B:Q.495, B:Q.495, B:L.497

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 beta chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

beta-hexosaminidase beta chain

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