SMTL ID : 4do4.1

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 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: 2 residues within 4Å: Chain A: N.107, F.142 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 Water bridges: B:D.2 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 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.368, A:N.368 NAG.15: 2 residues within 4Å: Chain B: E.366, N.368 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.366, B:N.368, B:N.368

2 x DJN: N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide(Non-covalent)

DJN.6: 15 residues within 4Å: Chain A: W.16, D.61, D.62, Y.102, C.110, M.111, K.137, D.139, S.171, A.174, Y.175, R.196, D.200 Ligands: GOL.10, ACY.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.174, A:R.196 Hydrogen bonds: A:D.62, A:D.62, A:K.137, A:K.137, A:D.139, A:S.171, A:R.196, A:R.196, A:D.200, A:D.200 DJN.16: 14 residues within 4Å: Chain B: W.16, D.61, D.62, Y.102, C.110, M.111, K.137, D.139, S.171, A.174, Y.175, R.196, D.200 Ligands: GOL.23 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.174, B:R.196 Hydrogen bonds: B:D.62, B:D.62, B:Y.102, B:K.137, B:K.137, B:D.139, B:S.171, B:Y.175, B:R.196, B:R.196, B:D.200, B:D.200

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

CIT.7: 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, A:D.77 Salt bridges: A:R.80 CIT.17: 7 residues within 4Å: Chain B: I.23, N.24, C.25, D.26, D.77, K.79, R.80 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.79 Hydrogen bonds: B:I.23, B:C.25, B:D.26, B:D.26, B:D.26 Water bridges: B:D.77 Salt bridges: B:R.80

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: M.39, E.40, D.43, Y.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.43 Water bridges: A:Q.36, A:E.40, A:Y.91 GOL.9: 3 residues within 4Å: Chain A: M.111, G.112, Y.113 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: A.174, Y.175, D.199, D.200 Ligands: DJN.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.200, A:D.200 Water bridges: A:D.200 GOL.12: 6 residues within 4Å: Chain A: L.306, R.327, T.328, D.329 Chain B: R.20, Q.202 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.20, B:Q.202, A:T.328, A:T.328 GOL.13: 5 residues within 4Å: Chain A: L.209, N.213, E.308, Y.310, C.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.209, A:E.308, A:Y.310, A:Y.310 GOL.14: 7 residues within 4Å: Chain A: P.29, C.32, S.34, E.35, Q.36, K.79, R.80 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.29, A:S.34, A:Q.36, A:K.79 Water bridges: A:C.32, A:E.35, A:Q.36 GOL.18: 5 residues within 4Å: Chain B: L.209, N.213, E.308, Y.310, C.326 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.209, B:Y.310, B:Y.310 Water bridges: B:R.299 GOL.19: 3 residues within 4Å: Chain B: F.108, G.112, F.142 No protein-ligand interaction detected (PLIP) GOL.20: 3 residues within 4Å: Chain B: M.111, G.112, Y.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.111 Water bridges: B:I.65, B:G.66 GOL.21: 4 residues within 4Å: Chain B: A.174, Y.175, D.199, D.200 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.174, B:D.199, B:D.200, B:D.200 GOL.22: 6 residues within 4Å: Chain A: R.20, Q.202 Chain B: L.306, R.327, T.328, D.329 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.20, A:Q.202, B:T.328, B:T.328 GOL.23: 4 residues within 4Å: Chain B: W.16, C.110, M.111 Ligands: DJN.16 No protein-ligand interaction detected (PLIP) GOL.24: 9 residues within 4Å: Chain B: L.6, T.8, P.9, P.10, M.11, G.54, T.56, Y.57, Q.290 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.8, B:T.8, B:M.11, B:M.11, B:T.56 Water bridges: B:L.6, B:Q.7

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.11: 4 residues within 4Å: Chain A: W.16, C.110, M.111 Ligands: DJN.6 No protein-ligand interaction detected (PLIP)

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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