SMTL ID : 3gxt.1

Crystal structure of alpha-galactosidase A at pH 4.5 complexed with 1-deoxygalactonijirimycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

3 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: 6 residues within 4Å: Chain A: N.108, F.118, Y.142, C.143, D.144, N.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.144 NAG-NAG.2: 4 residues within 4Å: Chain A: D.2, N.161, G.164 Ligands: MAN-MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.2 NAG-NAG.4: 4 residues within 4Å: Chain A: N.184, T.186, E.187, Q.190 No protein-ligand interaction detected (PLIP)

1 x MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose(Non-functional Binders)

MAN-MAN.3: 1 residues within 4Å: Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-MAN-MAN.5: 4 residues within 4Å: Chain B: D.2, R.7, N.161, G.164 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.2, B:R.7

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-MAN.6: 3 residues within 4Å: Chain B: N.184, T.186, E.187 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.190

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

SO4.7: 5 residues within 4Å: Chain A: W.205, K.206 Chain B: W.205, K.206, K.209 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.206, B:W.205, B:K.206 Water bridges: A:K.209, B:K.209, B:K.209 Salt bridges: A:K.209, B:K.209 SO4.8: 5 residues within 4Å: Chain A: R.301, I.336, A.337, S.340, R.371 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.337, A:A.337, A:S.340 Water bridges: A:R.371 Salt bridges: A:R.301, A:R.371 SO4.9: 2 residues within 4Å: Chain A: H.94, R.165 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.165 SO4.12: 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 SO4.13: 4 residues within 4Å: Chain B: R.87, N.91, H.94, R.165 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.87, B:N.91 Salt bridges: B:H.94, B:R.165

2 x NOJ: 1-DEOXYNOJIRIMYCIN(Non-covalent)

NOJ.10: 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:K.137, A:K.137, A:E.172, A:R.196, A:R.196, A:D.200 NOJ.14: 12 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, K.137, D.139, E.172, R.196, D.200, D.235, M.236 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.61, B:D.62, B:D.62, B:Y.103, B:K.137, B:K.137, B:D.139, B:R.196, B:R.196, B:D.200, B:D.235

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.11: 3 residues within 4Å: Chain B: N.108, F.118, D.144 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.118 Hydrogen bonds: B:N.108, B:N.108, B:D.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lieberman, R.L. et al., Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Biochemistry (2009)

Release Date

2009-05-26

Peptides

Alpha-galactosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-galactosidase A

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