SMTL ID : 1ktc.1

The Structure of alpha-N-Acetylgalactosaminidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 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: 7 residues within 4Å: Chain A: E.2, N.3, G.4, N.161, G.164, R.165, P.166 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 7 residues within 4Å: Chain B: E.2, N.3, G.4, N.161, G.164, R.165, P.166 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.2

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

NAG.2: 4 residues within 4Å: Chain A: N.185, T.187, L.188, E.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.185, A:L.188, A:E.191 NAG.3: 2 residues within 4Å: Chain A: T.336, N.369 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.369 NAG.23: 4 residues within 4Å: Chain B: N.185, T.187, L.188, E.191 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.185, B:L.188, B:E.191 NAG.24: 2 residues within 4Å: Chain B: T.336, N.369 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.369

2 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.4: 13 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, G.112, K.138, D.140, S.172, A.175, Y.176, R.197, D.201 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.175 Hydrogen bonds: A:D.62, A:D.62, A:K.138, A:K.138, A:S.172, A:R.197, A:D.201, A:D.201, A:D.201 NGA.25: 13 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, G.112, K.138, D.140, S.172, A.175, Y.176, R.197, D.201 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.175 Hydrogen bonds: B:D.62, B:Y.103, B:K.138, B:K.138, B:S.172, B:Y.176, B:R.197, B:D.201, B:D.201, B:D.201

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: E.27, D.28, P.29, R.30, Q.31 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.30, A:Q.31, A:Q.31 Water bridges: A:R.30, A:R.30 Salt bridges: A:R.30 SO4.6: 3 residues within 4Å: Chain A: S.145, G.146, Q.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.146, A:Q.177 Water bridges: A:K.147, A:K.147 SO4.7: 3 residues within 4Å: Chain A: R.251, Y.356, S.357 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.251, A:R.251 Salt bridges: A:R.251 SO4.8: 2 residues within 4Å: Chain A: H.307, R.327 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.327 Salt bridges: A:H.307, A:R.327 SO4.9: 2 residues within 4Å: Chain A: R.51, R.96 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.51, A:R.96 SO4.26: 5 residues within 4Å: Chain B: E.27, D.28, P.29, R.30, Q.31 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.28, B:R.30, B:Q.31, B:Q.31 Water bridges: B:R.30, B:R.30 Salt bridges: B:R.30 SO4.27: 3 residues within 4Å: Chain B: S.145, G.146, Q.177 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.146, B:Q.177 Water bridges: B:K.147, B:K.147 SO4.28: 3 residues within 4Å: Chain B: R.251, Y.356, S.357 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.247, B:R.251 Salt bridges: B:R.251 SO4.29: 2 residues within 4Å: Chain B: H.307, R.327 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.327 Salt bridges: B:H.307, B:R.327 SO4.30: 2 residues within 4Å: Chain B: R.51, R.96 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.51, B:R.96

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: D.354, K.359, T.371, V.372, W.382 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: Q.220, D.221, R.299, R.300 Ligands: GOL.17 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: P.77, R.84, G.85, I.86, K.87, A.88, W.132 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: Q.317, Y.383, C.385 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: S.316, Q.317 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: I.301, I.302, K.341, L.342 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain A: W.215, T.218, N.219 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain A: F.217, T.218, Q.220, R.300, K.303 Ligands: GOL.11 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain A: L.312, P.314, L.315, A.318, A.319, S.320 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain A: I.361, F.370, T.371 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain B: D.354, K.359, T.371, V.372, W.382 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain B: Q.220, D.221, R.299, R.300 Ligands: GOL.38 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain B: P.77, R.84, G.85, I.86, K.87, A.88, W.132 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain B: Q.317, Y.383, C.385 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain B: S.316, Q.317 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain B: I.301, I.302, K.341, L.342 Ligand excluded by PLIP GOL.37: 3 residues within 4Å: Chain B: W.215, T.218, N.219 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain B: F.217, T.218, Q.220, R.300, K.303 Ligands: GOL.32 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain B: L.312, P.314, L.315, A.318, A.319, S.320 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain B: I.361, F.370, T.371 Ligand excluded by PLIP

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

ACY.20: 3 residues within 4Å: Chain A: Q.282, N.283, R.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.284 Water bridges: A:R.284, A:R.284, A:L.285 Salt bridges: A:R.284 ACY.21: 2 residues within 4Å: Chain A: H.94, R.165 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.94, A:R.165 ACY.41: 3 residues within 4Å: Chain B: Q.282, N.283, R.284 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.284 Water bridges: B:R.284, B:R.284, B:L.285 Salt bridges: B:R.284 ACY.42: 2 residues within 4Å: Chain B: H.94, R.165 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.94, B:R.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garman, S.C. et al., The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases. Structure (2002)

Release Date

2002-03-15

Peptides

alpha-N-acetylgalactosaminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

alpha-N-acetylgalactosaminidase

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