SMTL ID : 6ibk.1

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfamidate ME763

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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.1: 6 residues within 4Å: Chain A: D.2, N.3, G.4, N.161, G.164, R.165 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 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 NAG-NAG.4: 3 residues within 4Å: Chain B: N.184, E.187, Q.190 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.5: 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:D.2

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

ACT.6: 6 residues within 4Å: Chain A: L.293, P.312, L.313, L.316, A.317, W.318 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.293, A:P.312 ACT.26: 6 residues within 4Å: Chain B: F.198, A.199, D.200, I.201, S.207, S.210 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.207, B:S.210 ACT.27: 3 residues within 4Å: Chain B: R.87, H.94, R.165 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.87, B:H.94, B:R.165

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

SO4.7: 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 SO4.8: 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 SO4.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.10: 3 residues within 4Å: Chain A: S.145, L.146, E.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.146, A:E.147 SO4.11: 2 residues within 4Å: Chain A: H.94, R.165 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.94, A:R.165 SO4.12: 2 residues within 4Å: Chain A: K.182, R.221 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.182, A:R.221 SO4.28: 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 SO4.29: 4 residues within 4Å: Chain B: L.1, D.2, R.189, Q.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.1 Salt bridges: B:R.189 SO4.30: 5 residues within 4Å: Chain B: Q.219, Q.299, L.300, R.301, Q.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.219, B:L.300, B:Q.302 SO4.31: 4 residues within 4Å: Chain B: G.85, I.86, R.87, W.131 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.86, B:R.87, B:W.131 Water bridges: B:A.77, B:W.131 SO4.32: 1 residues within 4Å: Chain B: K.209 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.209, B:E.327 Salt bridges: B:K.209

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

EDO.13: 4 residues within 4Å: Chain A: W.178, P.179, F.180, Q.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.180 EDO.14: 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.15: 3 residues within 4Å: Chain A: A.53, G.54, Q.290 No protein-ligand interaction detected (PLIP) EDO.16: 5 residues within 4Å: Chain A: S.273, Q.275 Chain B: W.246 Ligands: PEG.38, PEG.39 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.273, A:S.273, A:Q.275, B:W.246 Water bridges: A:Q.249, A:Q.249, A:S.273, B:S.245 EDO.17: 5 residues within 4Å: Chain A: F.198, A.199, D.200, S.207, S.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.200, A:S.210 EDO.18: 5 residues within 4Å: Chain A: A.278, L.279, D.282, P.358, V.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.278 Water bridges: A:K.360 EDO.19: 4 residues within 4Å: Chain A: N.184, Y.185, T.186, R.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.184, A:Y.185, A:T.186, A:T.186, A:R.221 EDO.20: 3 residues within 4Å: Chain A: R.361, R.373, H.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.361, A:H.375, A:H.375 EDO.33: 3 residues within 4Å: Chain B: S.370, R.371, R.373 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.371, B:R.373 EDO.34: 3 residues within 4Å: Chain B: T.335, R.371, R.373 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.371, B:R.373 EDO.35: 3 residues within 4Å: Chain B: A.53, I.286, Q.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.53 EDO.36: 5 residues within 4Å: Chain B: A.278, L.279, D.282, P.358, V.359 No protein-ligand interaction detected (PLIP)

2 x YTW: (3~{a}~{R},4~{S},5~{S},6~{S},7~{R},7~{a}~{S})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydro-3~{H}-benzo[d][1,2,3]oxathiazole-4,5,6-triol(Non-covalent)

YTW.21: 12 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, E.172, Y.176, R.196, D.200 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.16 Hydrogen bonds: A:D.61, A:D.62, A:A.112, A:K.137, A:E.172, A:R.196, A:R.196, A:D.200 Water bridges: A:D.200, A:D.235 YTW.37: 11 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, K.137, D.139, E.172, Y.176, R.196, D.200 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.16 Hydrogen bonds: B:D.61, B:D.62, B:D.62, B:K.137, B:E.172, B:R.196, B:R.196 Water bridges: B:D.200, B:D.200, B:D.235

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

PEG.22: 4 residues within 4Å: Chain A: G.85, I.86, R.87, W.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.86, A:R.87, A:R.87, A:W.131 PEG.23: 6 residues within 4Å: Chain A: P.358, R.361, H.375, I.376, N.377, V.382 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.361, A:N.377 Water bridges: A:N.247, A:R.361, A:T.381 PEG.24: 4 residues within 4Å: Chain A: W.16, M.20, C.21, A.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.21, A:C.21 PEG.38: 10 residues within 4Å: Chain A: L.244, S.245, W.246 Chain B: L.244, S.245, W.246, Q.249, S.273, Q.275 Ligands: EDO.16 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:W.246, B:Q.249, B:S.273, B:S.273, A:W.246, A:Q.249 Water bridges: A:N.247 PEG.39: 7 residues within 4Å: Chain A: G.240, N.241, F.242 Chain B: W.246, N.247, N.377 Ligands: EDO.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.247, B:N.377, A:G.240

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

NAG.25: 6 residues within 4Å: Chain B: N.108, F.118, Y.142, C.143, D.144, N.148 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.118, B:N.148 Hydrogen bonds: B:N.108, B:D.144, B:N.148

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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