SMTL ID : 5i85.1 (1 other biounit)

aSMase with zinc and phosphocholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

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: 4 residues within 4Å: Chain A: T.242, R.243, N.289 Ligands: SO4.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.243

1 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.123, N.129, I.130, S.131, N.349, T.351, Q.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.131, A:Q.358

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.3: 7 residues within 4Å: Chain A: I.472, N.474, T.476, Q.477, Q.488, F.526, G.531 No protein-ligand interaction detected (PLIP)

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

NAG.4: 1 residues within 4Å: Chain A: N.40 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: S.127, N.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.127, A:S.127, A:S.127, A:N.129 NAG.6: 5 residues within 4Å: Chain A: P.325, Y.326, P.327, N.457 Ligands: SO4.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.326

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 7 residues within 4Å: Chain A: D.160, D.232, N.272, H.379, H.411 Ligands: ZN.8, PC.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.232, A:H.379, A:H.411 ZN.8: 6 residues within 4Å: Chain A: D.160, H.162, D.232, H.413 Ligands: ZN.7, PC.20 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.160, A:H.162, A:D.232, A:H.413

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

SO4.9: 3 residues within 4Å: Chain A: H.384, H.411 Ligands: PC.20 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.384, A:H.411 SO4.10: 2 residues within 4Å: Chain A: K.59, N.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.62 Salt bridges: A:K.59 SO4.11: 3 residues within 4Å: Chain A: Q.86, S.87, H.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.86 Salt bridges: A:H.90 SO4.12: 2 residues within 4Å: Chain A: K.141, S.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.144 Salt bridges: A:K.141 SO4.13: 4 residues within 4Å: Chain A: R.102, I.286, E.287, H.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.287, A:E.287 Salt bridges: A:R.102, A:H.290 SO4.14: 6 residues within 4Å: Chain A: P.537, C.538, G.539, T.540, P.541, C.542 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.539, A:C.542 SO4.15: 3 residues within 4Å: Chain A: P.534, S.535, E.536 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.535, A:E.536 SO4.16: 4 residues within 4Å: Chain A: G.516, D.517, M.518, Q.519 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.518, A:Q.519 Water bridges: A:G.516 SO4.17: 2 residues within 4Å: Chain A: R.515, G.516 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.515, A:R.515 Salt bridges: A:R.515 SO4.18: 3 residues within 4Å: Chain A: D.94 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) SO4.19: 4 residues within 4Å: Chain A: D.225, Y.326, N.457 Ligands: NAG.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.225, A:Y.326, A:N.457 Water bridges: A:N.457, A:N.457

1 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.20: 12 residues within 4Å: Chain A: D.160, H.162, D.232, H.236, N.272, H.273, H.379, H.411, H.413 Ligands: ZN.7, ZN.8, SO4.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.232, A:N.272, A:N.272 Salt bridges: A:H.162, A:H.236, A:H.273, A:H.411, A:H.413 pi-Cation interactions: A:H.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y.F. et al., Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease. Nat Commun (2016)

Release Date

2016-09-07

Peptides

Sphingomyelin phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sphingomyelin phosphodiesterase

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