SMTL ID : 5i81.2 (1 other biounit)

aSMase with zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: 6 residues within 4Å: Chain A: L.91, Q.241, T.242, R.243, N.289 Ligands: BMA.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.91 Hydrogen bonds: A:R.243 NAG-NAG.24: 6 residues within 4Å: Chain B: L.91, Q.241, T.242, R.243, N.289 Ligands: BMA.29 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.91 Hydrogen bonds: B:R.243

2 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.2: 5 residues within 4Å: Chain A: D.123, N.349, T.351 Ligands: MAN-BMA.3, MAN-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 5 residues within 4Å: Chain B: D.123, N.349, T.351 Ligands: MAN-BMA.26, MAN-BMA.26 No protein-ligand interaction detected (PLIP)

2 x MAN- BMA: beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose(Non-covalent)

MAN-BMA.3: 5 residues within 4Å: Chain A: N.129, I.130, S.131 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.130 MAN-BMA.26: 5 residues within 4Å: Chain B: N.129, I.130, S.131 Ligands: NAG-NAG-BMA.25, NAG-NAG-BMA.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.130

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.4: 3 residues within 4Å: Chain A: N.40 Chain B: K.78, I.79 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: S.127, W.128, 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.7: 3 residues within 4Å: Chain A: Y.326, N.457 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.326 Hydrogen bonds: A:N.457 NAG.8: 1 residues within 4Å: Ligands: NAG.7 No protein-ligand interaction detected (PLIP) NAG.9: 7 residues within 4Å: Chain A: N.474, T.476, Q.477, Q.488, F.526, G.531 Ligands: NAG.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.526 Hydrogen bonds: A:N.474, A:Q.488 Water bridges: A:N.474, A:G.531 NAG.10: 1 residues within 4Å: Ligands: NAG.9 No protein-ligand interaction detected (PLIP) NAG.27: 3 residues within 4Å: Chain A: K.78, I.79 Chain B: N.40 No protein-ligand interaction detected (PLIP) NAG.28: 3 residues within 4Å: Chain B: S.127, W.128, N.129 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.127, B:S.127, B:S.127, B:N.129 NAG.30: 3 residues within 4Å: Chain B: Y.326, N.457 Ligands: NAG.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.326 Hydrogen bonds: B:N.457 NAG.31: 1 residues within 4Å: Ligands: NAG.30 No protein-ligand interaction detected (PLIP) NAG.32: 7 residues within 4Å: Chain B: N.474, T.476, Q.477, Q.488, F.526, G.531 Ligands: NAG.33 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.526 Hydrogen bonds: B:N.474, B:Q.488 Water bridges: B:N.474, B:G.531 NAG.33: 1 residues within 4Å: Ligands: NAG.32 No protein-ligand interaction detected (PLIP)

2 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.6: 1 residues within 4Å: Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP) BMA.29: 1 residues within 4Å: Ligands: NAG-NAG.24 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.11: 6 residues within 4Å: Chain A: D.160, D.232, N.272, H.379, H.411 Ligands: ZN.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.232, A:H.379, A:H.411, H2O.4 ZN.12: 5 residues within 4Å: Chain A: D.160, H.162, D.232, H.413 Ligands: ZN.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.160, A:D.232, A:H.413, H2O.4 ZN.34: 6 residues within 4Å: Chain B: D.160, D.232, N.272, H.379, H.411 Ligands: ZN.35 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.232, B:H.379, B:H.411, H2O.11 ZN.35: 5 residues within 4Å: Chain B: D.160, H.162, D.232, H.413 Ligands: ZN.34 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.160, B:D.232, B:H.413, H2O.11

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

SO4.13: 2 residues within 4Å: Chain A: H.384, H.411 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: K.59, N.62 Chain B: K.59, N.62 Ligands: SO4.37 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: Q.86, S.87, H.90 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: K.141, S.144 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain A: R.102, F.285, I.286, E.287, H.290 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain A: S.126, S.127 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain A: P.537, C.538, G.539, T.540, P.541, C.542 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: P.534, S.535, E.536 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain A: T.412, Y.442, I.443 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain A: G.516, D.517, M.518, Q.519 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain A: R.515, G.516 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain B: H.384, H.411 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain A: K.59, N.62 Chain B: K.59, N.62 Ligands: SO4.14 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain B: Q.86, S.87, H.90 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain B: K.141, S.144 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain B: R.102, F.285, I.286, E.287, H.290 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain B: S.126, S.127 Ligand excluded by PLIP SO4.42: 6 residues within 4Å: Chain B: P.537, C.538, G.539, T.540, P.541, C.542 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain B: P.534, S.535, E.536 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain B: T.412, Y.442, I.443 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain B: G.516, D.517, M.518, Q.519 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain B: R.515, G.516 Ligand excluded by PLIP

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Sphingomyelin phosphodiesterase

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