SMTL ID : 3h53.1

Crystal Structure of human alpha-N-acetylgalactosaminidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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: 3 residues within 4Å: Chain A: N.107, F.142, 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 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: 7 residues within 4Å: Chain B: D.2, N.3, G.4, N.160, G.163, R.164, P.165 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: 1 residues within 4Å: Chain B: N.107 No protein-ligand interaction detected (PLIP)

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: I.23, N.24, C.25, D.26, R.80 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: Q.36, M.39, E.40, D.43, Y.91 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: F.108, G.112, F.142 Ligands: GOL.8 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: M.111, G.112, Y.113 Ligands: GOL.7 Ligand excluded by 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 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: A.174, Y.175, R.196, Y.198, D.199, D.200 Ligands: GOL.11 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: W.16, C.110, M.111, D.200 Ligands: GOL.10, GOL.16 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: R.327, T.328, D.329 Chain B: R.20, Q.202 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: N.31, D.268, R.270, T.271 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: L.209, N.213, V.216, R.299, E.308, Y.310, C.326 Ligand excluded by PLIP GOL.16: 10 residues within 4Å: Chain A: W.16, D.61, D.62, Y.102, C.110, K.137, D.139, R.196, D.200 Ligands: GOL.11 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: I.23, N.24, C.25, D.26, K.79, R.80 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: F.108, G.112, F.142 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain B: M.111, G.112, Y.113 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: A.174, Y.175, R.196, Y.198, D.199, D.200 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: R.20, Q.202 Chain B: L.306, R.327, T.328, D.329 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain B: W.16, D.61, D.62, Y.102, C.110, K.137, D.139, R.196, D.200 Ligand excluded by PLIP

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

NAG.15: 2 residues within 4Å: Chain A: E.366, N.368 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.368 Water bridges: A:N.368, A:N.368, A:N.368, A:N.368 NAG.22: 2 residues within 4Å: Chain B: E.366, N.368 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.368 Water bridges: 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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