SMTL ID : 8k7f.1

Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R,5R)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 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.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 NAG-NAG-BMA-MAN.3: 7 residues within 4Å: Chain B: D.2, N.3, G.4, R.7, N.161, G.164, R.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.7, B:D.2 Water bridges: B:G.4, B:R.7

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

NAG-NAG.2: 4 residues within 4Å: Chain A: N.184, T.186, E.187, Q.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.190

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

NAG.4: 6 residues within 4Å: Chain A: N.108, F.118, Y.142, C.143, D.144, N.148 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.118 Hydrogen bonds: A:D.144, A:D.144, A:N.148 Water bridges: A:D.144 NAG.7: 3 residues within 4Å: Chain B: N.108, F.118, N.148 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.118 Hydrogen bonds: B:N.108, B:N.148 NAG.8: 3 residues within 4Å: Chain B: N.184, E.187, Q.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.184, B:Q.190 Water bridges: B:N.184, B:N.184

2 x VMF: (2~{R},3~{R},4~{S},5~{R})-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol(Non-covalent)

VMF.5: 13 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, E.172, L.175, Y.176, R.196, D.200 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.61, A:D.62, A:D.62, A:A.112, A:K.137, A:D.139, A:R.196, A:R.196 Water bridges: A:K.137, A:D.200, A:D.235, A:D.235 VMF.9: 12 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, K.137, D.139, E.172, L.175, Y.176, R.196, D.200 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.61, B:D.62, B:D.62, B:A.112, B:K.137, B:D.139, B:D.139, B:Y.176, B:R.196, B:R.196 Water bridges: B:K.137, B:D.200, B:D.235, B:D.235

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

SO4.6: 5 residues within 4Å: Chain A: R.301, I.336, A.337, S.340, R.371 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.337, A:S.340 Water bridges: A:R.301, A:R.301, A:R.301 Salt bridges: A:R.301, A:R.371 SO4.10: 6 residues within 4Å: Chain B: R.301, T.335, I.336, A.337, S.340, R.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.337, B:S.340 Salt bridges: B:R.301, B:R.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H.Y. et al., Mechanistic Insights into Dibasic Iminosugars as pH-Selective Pharmacological Chaperones to Stabilize Human alpha-Galactosidase. Jacs Au (2024)

Release Date

2024-04-10

Peptides

Alpha-galactosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-galactosidase A

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