SMTL ID : 3tv8.1

Pharmacological Chaperoning in Human alpha-Galactosidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-dimer

Ligands

1 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(Post Translational Modification)

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: D.2, N.3, G.4, N.161, G.164, R.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.2

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 4 residues within 4Å: Chain B: D.2, G.4, N.161, R.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.2

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

NAG.3: 6 residues within 4Å: Chain A: N.108, F.118, Y.142, C.143, D.144, N.148 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.118 Hydrogen bonds: A:D.144, A:D.144 NAG.4: 2 residues within 4Å: Chain A: N.184, Q.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.184, A:Q.190 NAG.9: 4 residues within 4Å: Chain B: N.108, F.118, Y.142, N.148 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.118 Hydrogen bonds: B:N.108 NAG.10: 2 residues within 4Å: Chain B: N.184, E.187 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.184

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

SO4.5: 5 residues within 4Å: Chain A: R.301, I.336, A.337, S.340, R.371 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.335, A:A.337, A:S.340 Salt bridges: A:R.301, A:R.371 SO4.11: 6 residues within 4Å: Chain B: R.301, T.335, I.336, A.337, S.340, R.371 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.335, B:A.337, B:S.340 Salt bridges: B:R.301, B:R.371 SO4.12: 2 residues within 4Å: Chain B: S.370, R.371 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.371, B:R.371

3 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.6: 9 residues within 4Å: Chain A: L.244, S.245, W.246, Q.249 Chain B: N.241, L.244, S.245, W.246, Q.249 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.241, B:W.246, A:L.244, A:W.246, A:Q.249 2PE.7: 3 residues within 4Å: Chain A: L.363, F.365, Y.366 No protein-ligand interaction detected (PLIP) 2PE.13: 3 residues within 4Å: Chain B: L.363, F.365, Y.366 No protein-ligand interaction detected (PLIP)

2 x DGJ: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

DGJ.8: 11 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, E.172, Y.176, R.196, D.200 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:K.137, A:K.137, A:Y.176, A:R.196, A:R.196, A:D.200 DGJ.14: 10 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, K.137, E.172, Y.176, R.196, D.200 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.62, B:D.62, B:Y.103, B:K.137, B:K.137, B:E.172, B:R.196, B:R.196, B:D.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guce, A.I. et al., The molecular basis of pharmacological chaperoning in human alpha-galactosidase. Chem.Biol. (2011)

Release Date

2012-01-04

Peptides

Alpha-galactosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-galactosidase A

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