SMTL ID : 6ibm.1

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfate ME776

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

3 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: 7 residues within 4Å: Chain A: D.2, N.3, G.4, N.161, G.164, R.165 Ligands: EDO.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.2 NAG-NAG-BMA.3: 6 residues within 4Å: Chain A: N.108, F.118, Y.142, C.143, D.144, N.148 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 6 residues within 4Å: Chain B: 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.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 NAG-NAG.5: 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- MAN: alpha-D-mannopyranose-(1-2)-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-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:D.2

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

PEG.7: 8 residues within 4Å: Chain A: L.244, S.245, W.246, Q.249 Chain B: L.244, S.245, W.246, Q.249 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:W.246, A:Q.249, B:W.246, B:Q.249 Water bridges: A:L.244, B:N.241 PEG.8: 6 residues within 4Å: Chain A: H.84, G.85, I.86, R.87, Q.88, W.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.84, A:I.86, A:Q.88

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

ACT.9: 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 ACT.10: 2 residues within 4Å: Chain A: S.314, G.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.315 ACT.11: 6 residues within 4Å: Chain A: F.198, A.199, D.200, I.201, S.207, S.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.210 ACT.25: 3 residues within 4Å: Chain B: R.87, H.94, R.165 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.94, B:R.165

6 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:D.2 Salt bridges: A:R.189 SO4.14: 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 SO4.26: 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 SO4.27: 4 residues within 4Å: Chain B: L.1, D.2, R.189, Q.190 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.1, B:D.2 Water bridges: B:D.2, B:R.7 Salt bridges: B:R.189 SO4.28: 4 residues within 4Å: Chain B: Q.299, L.300, R.301, Q.302 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.302

2 x HF8: [(1~{S},2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate(Covalent)

HF8.15: 13 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, C.141, E.172, Y.176, R.196, D.200 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.16, A:D.139 Hydrogen bonds: A:D.62, A:D.62, A:A.112, A:K.137, A:K.137, A:R.196, A:R.196 Water bridges: A:Y.176, A:D.200, A:D.200, A:D.235 HF8.29: 13 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, C.141, E.172, Y.176, R.196, D.200 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.16, B:D.139 Hydrogen bonds: B:D.62, B:D.62, B:A.112, B:K.137, B:K.137, B:R.196, B:R.196, B:D.200 Water bridges: B:D.200, B:D.235

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

EDO.16: 3 residues within 4Å: Chain A: A.53, I.286, Q.290 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: G.240, N.241, F.242, H.271 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: Q.88, N.91, Y.92 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: C.143, D.144, S.145, L.146, L.149, Y.176 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: L.5, A.6, T.8, T.10, Y.57, V.168 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: Y.176, P.179 Ligands: EDO.22 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: L.175, F.198, A.199 Ligands: EDO.21 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: E.43, Y.92, K.96 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: L.1, S.157, L.158, Q.190, Y.191 Ligands: NAG-NAG-BMA.1 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: A.53, G.54, I.286, Q.290 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: R.87, W.131 Ligands: EDO.34 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: W.246, A.278, L.279, D.282, L.357, P.358 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain B: S.370, R.371 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: A.77, G.85, I.86, R.87, W.131 Ligands: EDO.31 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: F.198, A.199, D.200, I.201, S.207, S.210 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: T.8, P.9, T.10, M.11, G.54, Q.290 Ligand excluded by PLIP EDO.37: 1 residues within 4Å: Chain B: R.270 Ligand excluded by PLIP EDO.38: 1 residues within 4Å: Chain B: D.52 Ligand excluded by PLIP

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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