SMTL ID : 4do6.1

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 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: 4 residues within 4Å: Chain A: N.107, F.142, S.143, T.144 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN: 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.2: 7 residues within 4Å: Chain A: D.2, N.3, G.4, N.160, G.163, R.164, P.165 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.2 NAG-NAG-BMA-MAN-MAN.4: 6 residues within 4Å: Chain B: D.2, N.3, G.4, N.160, G.163, R.164 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.2

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 3 residues within 4Å: Chain B: N.107, F.142, S.143 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: E.366, N.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.366 NAG.9: 2 residues within 4Å: Chain B: E.366, N.368 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.366, B:N.368 Water bridges: B:N.368

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 7 residues within 4Å: Chain A: I.23, N.24, C.25, D.26, D.77, K.79, R.80 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.79 Hydrogen bonds: A:I.23, A:C.25, A:D.26, A:D.26 Water bridges: A:D.77 Salt bridges: A:K.79, A:R.80

3 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.7: 6 residues within 4Å: Chain A: L.306, R.327, T.328, D.329 Chain B: R.20, Q.202 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.20, B:Q.202, B:Q.202, A:T.328, A:T.328, A:T.328, A:D.329 Water bridges: A:K.304, A:R.327 GLC.8: 7 residues within 4Å: Chain A: E.247, R.250, D.353, Y.355, S.356, V.378, V.379 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.247, A:R.250, A:D.353, A:S.356 Water bridges: A:D.353 Salt bridges: A:R.250 GLC.12: 7 residues within 4Å: Chain B: E.247, R.250, D.353, Y.355, S.356, V.378, V.379 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.247, B:R.250, B:D.353, B:S.356 Water bridges: B:D.353, B:M.380 Salt bridges: B:R.250

2 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)(Non-functional Binders)

2PE.10: 2 residues within 4Å: Chain B: M.111, G.112 No protein-ligand interaction detected (PLIP) 2PE.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.11: 6 residues within 4Å: Chain A: R.20, Q.202 Chain B: L.306, R.327, T.328, D.329 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.20, A:Q.202, A:Q.202, A:Q.202, B:T.328, B:T.328, B:T.328 Water bridges: B:R.327, B:R.327 Salt bridges: B:R.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, N.E. et al., Pharmacological chaperones for human alpha-N-acetylgalactosaminidase. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-10-10

Peptides

Alpha-N-acetylgalactosaminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-N-acetylgalactosaminidase

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