SMTL ID : 3h55.1

Crystal Structure of human alpha-N-acetylgalactosaminidase, Complex with Galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-FUC.1: 5 residues within 4Å: Chain A: N.107, F.142, S.143, T.144, E.147 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 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.2, A:D.2, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.368 Water bridges: A:E.366, A:N.368 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

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

GLA.6: 11 residues within 4Å: Chain A: W.16, D.61, D.62, Y.102, C.110, M.111, K.137, D.139, R.196, D.200 Ligands: GLA.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:M.111, A:K.137, A:K.137, A:R.196, A:R.196, A:D.200, A:D.200 Water bridges: A:D.139, A:Y.175 GLA.7: 7 residues within 4Å: Chain A: C.141, A.174, Y.175, Y.198, D.199, D.200 Ligands: GLA.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.198 Water bridges: A:A.174, A:Y.175, A:D.199, A:D.200 GLA.10: 11 residues within 4Å: Chain B: W.16, D.61, D.62, Y.102, C.110, M.111, K.137, D.139, R.196, D.200 Ligands: GLA.11 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.62, B:D.62, B:Y.102, B:M.111, B:K.137, B:K.137, B:R.196, B:R.196, B:D.200, B:D.200 Water bridges: B:D.139, B:Y.175 GLA.11: 9 residues within 4Å: Chain B: C.110, C.141, A.174, Y.175, R.196, Y.198, D.199, D.200 Ligands: GLA.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.174, B:Y.198, B:Y.198, B:D.199 Water bridges: B:Y.175, B:D.200 Salt bridges: B:R.196

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

CIT.8: 6 residues within 4Å: Chain A: H.93, G.96, L.97, K.98, D.134, R.164 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.93 Hydrogen bonds: A:K.98, A:K.98 Water bridges: A:H.93, A:G.96, A:D.134, A:R.164, A:R.164 Salt bridges: A:H.93, A:H.93, A:K.98, A:R.164 CIT.12: 6 residues within 4Å: Chain B: H.93, G.96, L.97, K.98, D.134, R.164 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:K.98 Hydrogen bonds: B:G.96, B:K.98, B:K.98 Water bridges: B:H.93, B:G.96, B:D.134, B:R.164 Salt bridges: B:H.93, B:H.93, B:K.98, B:R.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, N.E. et al., The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases. J.Mol.Biol. (2009)

Release Date

2009-10-20

Peptides

Alpha-N-acetylgalactosaminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-N-acetylgalactosaminidase

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