SMTL ID : 3igu.1

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

1 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: 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, 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 Water bridges: 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: 1 residues within 4Å: Chain B: N.107 No protein-ligand interaction detected (PLIP)

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: I.23, N.24, C.25, D.26, R.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.25, A:D.26, A:D.26 Water bridges: A:K.79 GOL.6: 5 residues within 4Å: Chain A: Q.36, M.39, E.40, D.43, Y.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:Y.91 Water bridges: A:Y.91 GOL.7: 3 residues within 4Å: Chain A: F.108, G.112, F.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.112 GOL.8: 2 residues within 4Å: Chain A: M.111, G.112 No protein-ligand interaction detected (PLIP) GOL.9: 9 residues within 4Å: Chain A: L.6, T.8, P.9, P.10, M.11, G.54, T.56, Y.57, Q.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.8, A:M.11, A:G.54 Water bridges: A:T.8, A:T.56 GOL.10: 5 residues within 4Å: Chain A: Y.175, D.199, D.200 Ligands: GOL.11, 7JZ.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.200 Water bridges: A:D.200 GOL.11: 6 residues within 4Å: Chain A: W.16, C.110, M.111, D.200 Ligands: GOL.10, 7JZ.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.200 GOL.12: 5 residues within 4Å: Chain A: R.327, D.329 Chain B: W.16, R.20, M.111 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.20, A:R.327, A:D.329, A:D.329 Water bridges: B:C.21, B:C.21 GOL.13: 4 residues within 4Å: Chain A: N.31, D.268, R.270, T.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.31, A:D.268 Water bridges: A:D.268 GOL.14: 7 residues within 4Å: Chain A: L.209, N.213, V.216, R.299, E.308, Y.310, C.326 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.209, A:R.299, A:R.299, A:E.308, A:Y.310 GOL.17: 6 residues within 4Å: Chain B: I.23, N.24, C.25, D.26, K.79, R.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.23, B:C.25, B:D.26, B:D.26 GOL.18: 3 residues within 4Å: Chain B: F.108, G.112, F.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.112 GOL.19: 3 residues within 4Å: Chain B: M.111, G.112, Y.113 No protein-ligand interaction detected (PLIP) GOL.20: 4 residues within 4Å: Chain B: Y.175, D.199, D.200 Ligands: 7JZ.22 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.199, B:D.199, B:D.200 Water bridges: B:Y.175, B:R.196 GOL.21: 5 residues within 4Å: Chain A: R.20, Q.202 Chain B: R.327, T.328, D.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.328, B:T.328, B:T.328

2 x 7JZ: 2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose(Post Translational Modification)

7JZ.15: 14 residues within 4Å: Chain A: W.16, D.61, D.62, Y.102, C.110, M.111, K.137, D.139, S.171, Y.175, R.196, D.200 Ligands: GOL.10, GOL.11 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:M.111, A:K.137, A:K.137, A:R.196 Water bridges: A:K.137, A:D.200, A:D.235, A:D.235 Halogen bonds: A:S.171, A:D.200 7JZ.22: 13 residues within 4Å: Chain B: W.16, D.61, D.62, Y.102, C.110, M.111, K.137, D.139, S.171, Y.175, R.196, D.200 Ligands: GOL.20 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.62, B:D.62, B:M.111, B:K.137, B:K.137, B:R.196 Water bridges: B:K.137, B:D.200, B:D.235, B:D.235 Halogen bonds: B:S.171, B:D.200

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

NAG.16: 2 residues within 4Å: Chain A: E.366, N.368 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.366 Hydrogen bonds: A:E.366, A:N.368 Water bridges: A:N.368 NAG.23: 2 residues within 4Å: Chain B: E.366, N.368 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.366, B:N.368

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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