SMTL ID : 8k7j.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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.4: 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

3 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 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: G.107, N.108, F.118, Y.142, C.143, D.144, N.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.148 Water bridges: B:D.144 NAG-NAG.5: 4 residues within 4Å: Chain B: N.184, T.186, E.187, Q.190 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.186

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

NAG.6: 6 residues within 4Å: Chain A: N.108, F.118, Y.142, C.143, D.144, N.148 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.118, A:N.148 Hydrogen bonds: A:D.144, A:D.144, A:N.148 Water bridges: A:N.108

2 x VNB: (2~{R},3~{R},4~{S},5~{R})-2-[(dimethylamino)methyl]-5-(hydroxymethyl)pyrrolidine-3,4-diol(Non-covalent)

VNB.7: 12 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, K.137, D.139, E.172, L.175, Y.176, R.196, D.200 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.61, A:D.62, A:A.112, A:K.137, A:D.139, A:R.196 Water bridges: A:D.200, A:D.200 Salt bridges: A:D.139, A:E.172, A:D.200 VNB.12: 13 residues within 4Å: Chain B: 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 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 Water bridges: B:D.200, B:D.235 Salt bridges: B:D.139, B:E.172, B:D.200

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

SO4.8: 5 residues within 4Å: Chain A: R.301, I.336, A.337, S.340, R.371 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.337, A:S.340 Salt bridges: A:R.301, A:R.371 SO4.9: 5 residues within 4Å: Chain A: W.205, K.206, K.209 Chain B: W.205, K.206 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:W.205, B:K.206, A:W.205, A:K.206 Water bridges: B:K.209, B:K.209, A:K.209, A:K.209, A:K.209, A:K.209 Salt bridges: B:K.209, A:K.209 SO4.10: 4 residues within 4Å: Chain A: L.1, D.2, R.189, Q.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.2 Salt bridges: A:R.189 SO4.13: 5 residues within 4Å: Chain B: R.301, 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 SO4.14: 3 residues within 4Å: Chain B: R.87, H.94, R.165 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.87, B:R.87 Salt bridges: B:R.87, B:H.94, B:R.165

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.11: 10 residues within 4Å: Chain A: L.175, W.178, N.197, F.198, A.199, D.200, S.207, S.210, I.211, W.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.197, A:A.199, A:S.210

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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