SMTL ID : 3gxp.1

Crystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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.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

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: N.184, T.186, E.187, Q.190 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: G.107, N.108, F.118, Y.142, C.143, D.144, N.148 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: D.2, N.3, N.161, G.164, R.165 Ligands: MAN.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.2 NAG-NAG.5: 3 residues within 4Å: Chain B: N.184, E.187, Q.190 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.190

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

SO4.6: 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 SO4.11: 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 SO4.12: 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 SO4.13: 2 residues within 4Å: Chain B: H.94, R.165 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.94, B:R.165

2 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.7: 11 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, E.172, R.196, D.200 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.62, A:A.112, A:K.137, A:K.137, A:D.139, A:R.196, A:R.196, A:D.200, A:D.200 GLA.16: 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 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.62, B:K.137, B:K.137, B:E.172, B:R.196, B:R.196, B:D.200, B:D.200

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.8: 12 residues within 4Å: Chain A: S.204, W.205, K.206, K.209, G.243, E.327 Chain B: S.204, W.205, K.206, K.209, Q.248, E.327 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:W.205, B:K.206, A:K.206 Hydrogen bonds: B:K.209, B:Q.248, A:W.205, A:K.206, A:K.206, A:K.206, A:K.209, A:G.243, A:E.327

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

NAG.9: 7 residues within 4Å: Chain A: N.108, F.118, Y.142, C.143, D.144, N.148 Ligands: NAG.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.118, A:N.148 Hydrogen bonds: A:N.108, A:D.144 NAG.10: 2 residues within 4Å: Chain A: D.144 Ligands: NAG.9 No protein-ligand interaction detected (PLIP)

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

MAN.14: 2 residues within 4Å: Ligands: NAG-NAG.4, MAN.15 No protein-ligand interaction detected (PLIP) MAN.15: 1 residues within 4Å: Ligands: MAN.14 No protein-ligand interaction detected (PLIP)

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

2009-05-05

Peptides

Alpha-galactosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-galactosidase A

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