SMTL ID : 4nxs.1

Crystal structure of human alpha-galactosidase A in complex with 1-deoxygalactonojirimycin-pFPhT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

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.1: 5 residues within 4Å: Chain A: D.2, N.3, N.161, G.164, R.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.2 NAG-NAG.2: 5 residues within 4Å: Chain B: D.2, N.3, N.161, G.164, R.165 No protein-ligand interaction detected (PLIP)

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

SO4.3: 6 residues within 4Å: Chain A: R.301, T.335, 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 SO4.4: 5 residues within 4Å: Chain A: W.205, K.206 Chain B: W.205, K.206, K.209 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:W.205, A:K.206, B:W.205, B:K.206 Salt bridges: A:K.209, B:K.209 SO4.5: 3 residues within 4Å: Chain A: L.1, D.2, R.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.1 Salt bridges: A:R.189 SO4.9: 6 residues within 4Å: Chain B: R.301, T.335, 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 SO4.10: 3 residues within 4Å: Chain B: S.370, R.371, R.373 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.371, B:R.371 Salt bridges: B:R.373

4 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.118, A:N.148 Hydrogen bonds: A:D.144, A:D.144, A:N.148 NAG.7: 3 residues within 4Å: Chain A: N.184, T.186, E.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.187 NAG.11: 3 residues within 4Å: Chain B: N.184, T.186, E.187 No protein-ligand interaction detected (PLIP) NAG.12: 7 residues within 4Å: Chain B: G.107, N.108, F.118, Y.142, C.143, D.144, N.148 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.118 Hydrogen bonds: B:D.144, B:D.144

2 x 2OZ: (2R,3S,4R,5S)-N-(4-fluorophenyl)-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide(Non-covalent)

2OZ.8: 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.175, A:Y.176 Hydrogen bonds: A:D.61, A:D.62, A:Y.103, A:Y.103, A:K.137, A:K.137, A:D.139, A:E.172, A:R.196, A:D.200 2OZ.13: 13 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, K.137, D.139, E.172, L.175, Y.176, R.196, A.199, D.200 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.175, B:Y.176, B:A.199 Hydrogen bonds: B:D.61, B:D.62, B:K.137, B:E.172, B:E.172, B:R.196, B:D.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Y. et al., Molecular Basis of 1-Deoxygalactonojirimycin Arylthiourea Binding to Human alpha-Galactosidase A: Pharmacological Chaperoning Efficacy on Fabry Disease Mutants. Acs Chem.Biol. (2014)

Release Date

2014-06-11

Peptides

Alpha-galactosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-galactosidase A

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