SMTL ID : 6ibr.1

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol epoxide LWA481

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

2 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: 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.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.5: 4 residues within 4Å: Chain B: N.184, T.186, E.187, Q.190 No protein-ligand interaction detected (PLIP)

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.4: 5 residues within 4Å: Chain B: D.2, N.3, G.4, N.161, R.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.7

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

SO4.6: 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 SO4.7: 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 SO4.8: 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: 4 residues within 4Å: Chain A: G.85, I.86, R.87, W.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.86, A:R.87 Water bridges: A:G.85 SO4.22: 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 SO4.23: 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 SO4.24: 4 residues within 4Å: Chain B: G.85, I.86, R.87, W.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.86, B:R.87, B:W.131

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

EDO.10: 5 residues within 4Å: Chain A: T.10, M.11, G.54, Y.57, Q.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.11, A:Q.290 EDO.11: 7 residues within 4Å: Chain A: G.140, C.143, D.144, S.145, L.149, Y.176, F.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.140, A:D.144 EDO.12: 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.13: 6 residues within 4Å: Chain A: G.119, Y.120, Y.121, D.122, I.123, H.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.121, A:D.122, A:I.123, A:H.155 EDO.14: 5 residues within 4Å: Chain A: P.358, H.375, I.376, N.377, V.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.377 Water bridges: A:N.247, A:T.381 EDO.15: 3 residues within 4Å: Chain A: R.361, S.374, H.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.361, A:H.375, A:H.375 EDO.25: 7 residues within 4Å: Chain B: W.246, A.278, L.279, D.282, L.357, P.358, V.359 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.278, B:D.282, B:P.358 EDO.26: 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.18, B:R.18, B:D.268 EDO.27: 5 residues within 4Å: Chain B: D.52, A.53, G.54, I.286, Q.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.52

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

PEG.16: 8 residues within 4Å: Chain A: L.244, W.246, Q.249 Chain B: N.241, L.244, S.245, W.246, Q.249 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:L.244, A:W.246, A:Q.249, B:N.241, B:W.246, B:Q.249 Water bridges: B:N.247 PEG.17: 10 residues within 4Å: Chain A: L.14, S.170, D.233, D.235, M.236, L.237, W.256, P.262, L.263, F.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.170, A:D.235, A:L.237, A:F.264, A:F.264 PEG.18: 4 residues within 4Å: Chain A: R.189, D.224, V.225, A.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.226 PEG.28: 11 residues within 4Å: Chain A: S.204, W.205, G.243, Q.248, E.327, T.379 Chain B: D.203, S.204, W.205, G.243, Q.248 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:W.205, A:G.243, A:Q.248, A:E.327, B:W.205, B:Q.248 Water bridges: A:K.206, B:K.206

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

ACT.19: 6 residues within 4Å: Chain A: F.198, A.199, D.200, S.207, S.210, I.211 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.198, A:A.199, A:I.211 Hydrogen bonds: A:D.202, A:S.210 ACT.29: 2 residues within 4Å: Chain B: R.87, R.165 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.87, B:H.94, B:R.165 ACT.30: 4 residues within 4Å: Chain B: Q.219, Q.299, L.300, R.301 No protein-ligand interaction detected (PLIP) ACT.31: 2 residues within 4Å: Chain B: S.370, R.371 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.371 ACT.32: 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.33: 2 residues within 4Å: Chain B: T.335, R.371 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.335 Salt bridges: B:R.371

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

HBE.20: 10 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, K.137, D.139, E.172, R.196, D.200 9 PLIP interactions: 9 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:R.196, A:R.196, A:D.200 HBE.34: 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

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

NAG.21: 6 residues within 4Å: Chain B: N.108, F.118, Y.142, C.143, D.144, N.148 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.144, 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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