SMTL ID : 6ibt.1

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol aziridine ME737

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 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

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: N.108, F.118, Y.142, C.143, D.144, N.148 No protein-ligand interaction detected (PLIP)

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.2: 6 residues within 4Å: Chain A: D.2, N.3, G.4, N.161, G.164, R.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.2, A:D.2 NAG-NAG-BMA-MAN.3: 6 residues within 4Å: Chain B: D.2, N.3, G.4, N.161, G.164, R.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: 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.4: 2 residues within 4Å: Chain B: N.184, E.187 No protein-ligand interaction detected (PLIP)

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

NAG.5: 4 residues within 4Å: Chain A: N.184, T.186, E.187, Q.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.184, A:E.187, A:Q.190 NAG.24: 5 residues within 4Å: Chain B: N.108, F.118, Y.142, C.143, D.144 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.118 Hydrogen bonds: B:D.144, B:D.144

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: D.213, W.214, F.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.213 EDO.9: 4 residues within 4Å: Chain A: Q.299, L.300, R.301, Q.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.219 Water bridges: A:Q.302, A:Q.302 EDO.18: 9 residues within 4Å: Chain A: G.330, P.331 Chain B: R.18, F.19, D.30, S.31, D.268, R.270, H.271 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.18, B:R.18, B:D.268, B:R.270 EDO.19: 2 residues within 4Å: Chain B: L.293, S.314 No protein-ligand interaction detected (PLIP) EDO.20: 7 residues within 4Å: Chain B: P.9, T.10, M.11, G.54, Y.57, Q.290 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.11 EDO.21: 5 residues within 4Å: Chain B: A.53, G.54, I.286, Q.290 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.53 EDO.23: 1 residues within 4Å: Chain B: F.352 No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 9 residues within 4Å: Chain A: S.204, W.205, K.206, G.243, Q.248 Chain B: S.204, W.205, G.243, Q.248 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:W.205, B:Q.248, A:W.205, A:K.206, A:Q.248 Water bridges: B:K.206, A:W.205, A:E.327 PEG.8: 6 residues within 4Å: Chain A: H.84, G.85, I.86, R.87, Q.88, W.131 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.84, A:I.86, A:R.87, A:R.87, A:Q.88 PEG.11: 8 residues within 4Å: Chain A: L.244, W.246, Q.249 Chain B: L.244, S.245, W.246, Q.249, Q.275 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:W.246, B:Q.249, B:Q.275, A:L.244, A:W.246, A:Q.249 Water bridges: B:N.241, B:N.241, B:F.242

2 x H9T: (1~{S},2~{S},3~{S},4~{S},5~{R},6~{S})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol(Covalent)

H9T.10: 11 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, E.172, R.196, D.200 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.16 Hydrogen bonds: A:D.62, A:D.62, A:A.112, A:K.137, A:K.137, A:D.139, A:R.196, A:R.196, A:D.200 H9T.22: 12 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, E.172, Y.176, R.196, D.200 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.16 Hydrogen bonds: B:D.62, B:D.62, B:A.112, B:K.137, B:K.137, B:D.139, B:R.196, B:R.196, B:D.200

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

SO4.12: 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 SO4.13: 4 residues within 4Å: Chain A: L.1, D.2, R.189, Q.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.2 Water bridges: A:R.189 Salt bridges: A:R.189 SO4.14: 2 residues within 4Å: Chain A: H.94, R.165 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.94, A:H.94 Salt bridges: A:H.94, A:R.165 SO4.25: 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 SO4.26: 4 residues within 4Å: Chain B: L.1, D.2, R.189, Q.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.1, B:L.1 Water bridges: B:D.2 Salt bridges: B:R.189

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.15: 6 residues within 4Å: Chain A: F.198, A.199, D.200, S.207, S.210, I.211 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.198, A:A.199, A:I.211 Hydrogen bonds: A:D.202, A:S.210, A:S.210 ACT.16: 3 residues within 4Å: Chain A: A.53, I.286, Q.290 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.287 ACT.17: 1 residues within 4Å: Chain A: R.373 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.373 ACT.27: 2 residues within 4Å: Chain B: H.94, R.165 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.94, B:R.165 ACT.28: 6 residues within 4Å: Chain B: F.198, A.199, D.200, I.201, S.207, S.210 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.210 ACT.29: 5 residues within 4Å: Chain B: W.246, A.278, L.279, D.282, P.358 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.246 Hydrogen bonds: B:A.278, B:D.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Artola, M. et al., Alpha-d-Gal-cyclophellitol cyclosulfamidate is a Michaelis complex analog that stabilizes therapeutic lysosomal alpha-galactosidase A in Fabry disease. Chem Sci (2019)

Release Date

2019-10-09

Peptides

Alpha-galactosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-galactosidase A

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