SMTL ID : 5i85.2 (1 other biounit)

aSMase with zinc and phosphocholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 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 NAG-NAG-BMA.21: 4 residues within 4Å: Chain B: T.242, R.243, N.289 Ligands: SO4.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.243 NAG-NAG-BMA.41: 4 residues within 4Å: Chain C: T.242, R.243, N.289 Ligands: SO4.58 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.243 NAG-NAG-BMA.61: 4 residues within 4Å: Chain D: T.242, R.243, N.289 Ligands: SO4.78 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.243

4 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 NAG-NAG-BMA-MAN-MAN.22: 7 residues within 4Å: Chain B: D.123, N.129, I.130, S.131, N.349, T.351, Q.358 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.131, B:Q.358 NAG-NAG-BMA-MAN-MAN.42: 7 residues within 4Å: Chain C: D.123, N.129, I.130, S.131, N.349, T.351, Q.358 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.131, C:Q.358 NAG-NAG-BMA-MAN-MAN.62: 7 residues within 4Å: Chain D: D.123, N.129, I.130, S.131, N.349, T.351, Q.358 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.131, D:Q.358

4 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) NAG-NAG.23: 7 residues within 4Å: Chain B: I.472, N.474, T.476, Q.477, Q.488, F.526, G.531 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 7 residues within 4Å: Chain C: I.472, N.474, T.476, Q.477, Q.488, F.526, G.531 No protein-ligand interaction detected (PLIP) NAG-NAG.63: 7 residues within 4Å: Chain D: I.472, N.474, T.476, Q.477, Q.488, F.526, G.531 No protein-ligand interaction detected (PLIP)

12 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 NAG.24: 1 residues within 4Å: Chain B: N.40 No protein-ligand interaction detected (PLIP) NAG.25: 2 residues within 4Å: Chain B: S.127, 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.26: 5 residues within 4Å: Chain B: P.325, Y.326, P.327, N.457 Ligands: SO4.39 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.326 NAG.44: 1 residues within 4Å: Chain C: N.40 No protein-ligand interaction detected (PLIP) NAG.45: 2 residues within 4Å: Chain C: S.127, N.129 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.127, C:S.127, C:S.127, C:N.129 NAG.46: 5 residues within 4Å: Chain C: P.325, Y.326, P.327, N.457 Ligands: SO4.59 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.326 NAG.64: 1 residues within 4Å: Chain D: N.40 No protein-ligand interaction detected (PLIP) NAG.65: 2 residues within 4Å: Chain D: S.127, N.129 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.127, D:S.127, D:S.127, D:N.129 NAG.66: 5 residues within 4Å: Chain D: P.325, Y.326, P.327, N.457 Ligands: SO4.79 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.326

8 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 ZN.27: 7 residues within 4Å: Chain B: D.160, D.232, N.272, H.379, H.411 Ligands: ZN.28, PC.40 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.232, B:H.379, B:H.411 ZN.28: 6 residues within 4Å: Chain B: D.160, H.162, D.232, H.413 Ligands: ZN.27, PC.40 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.160, B:H.162, B:D.232, B:H.413 ZN.47: 7 residues within 4Å: Chain C: D.160, D.232, N.272, H.379, H.411 Ligands: ZN.48, PC.60 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.232, C:H.379, C:H.411 ZN.48: 6 residues within 4Å: Chain C: D.160, H.162, D.232, H.413 Ligands: ZN.47, PC.60 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.160, C:H.162, C:D.232, C:H.413 ZN.67: 7 residues within 4Å: Chain D: D.160, D.232, N.272, H.379, H.411 Ligands: ZN.68, PC.80 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.232, D:H.379, D:H.411 ZN.68: 6 residues within 4Å: Chain D: D.160, H.162, D.232, H.413 Ligands: ZN.67, PC.80 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.160, D:H.162, D:D.232, D:H.413

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

SO4.9: 3 residues within 4Å: Chain A: H.384, H.411 Ligands: PC.20 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: K.59, N.62 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: Q.86, S.87, H.90 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: K.141, S.144 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: R.102, I.286, E.287, H.290 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain A: P.537, C.538, G.539, T.540, P.541, C.542 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: P.534, S.535, E.536 Chain D: P.189, A.190 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: G.516, D.517, M.518, Q.519 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: R.515, G.516 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: D.94 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: D.225, Y.326, N.457 Ligands: NAG.6 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: H.384, H.411 Ligands: PC.40 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain B: K.59, N.62 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: Q.86, S.87, H.90 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain B: K.141, S.144 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain B: R.102, I.286, E.287, H.290 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain B: P.537, C.538, G.539, T.540, P.541, C.542 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain B: P.534, S.535, E.536 Chain C: P.189, A.190 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain B: G.516, D.517, M.518, Q.519 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain B: R.515, G.516 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain B: D.94 Ligands: NAG-NAG-BMA.21, NAG-NAG-BMA.21 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain B: D.225, Y.326, N.457 Ligands: NAG.26 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain C: H.384, H.411 Ligands: PC.60 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain C: K.59, N.62 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain C: Q.86, S.87, H.90 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain C: K.141, S.144 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain C: R.102, I.286, E.287, H.290 Ligand excluded by PLIP SO4.54: 6 residues within 4Å: Chain C: P.537, C.538, G.539, T.540, P.541, C.542 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain B: P.189, A.190 Chain C: P.534, S.535, E.536 Ligand excluded by PLIP SO4.56: 4 residues within 4Å: Chain C: G.516, D.517, M.518, Q.519 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain C: R.515, G.516 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain C: D.94 Ligands: NAG-NAG-BMA.41, NAG-NAG-BMA.41 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain C: D.225, Y.326, N.457 Ligands: NAG.46 Ligand excluded by PLIP SO4.69: 3 residues within 4Å: Chain D: H.384, H.411 Ligands: PC.80 Ligand excluded by PLIP SO4.70: 2 residues within 4Å: Chain D: K.59, N.62 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain D: Q.86, S.87, H.90 Ligand excluded by PLIP SO4.72: 2 residues within 4Å: Chain D: K.141, S.144 Ligand excluded by PLIP SO4.73: 4 residues within 4Å: Chain D: R.102, I.286, E.287, H.290 Ligand excluded by PLIP SO4.74: 6 residues within 4Å: Chain D: P.537, C.538, G.539, T.540, P.541, C.542 Ligand excluded by PLIP SO4.75: 5 residues within 4Å: Chain A: P.189, A.190 Chain D: P.534, S.535, E.536 Ligand excluded by PLIP SO4.76: 4 residues within 4Å: Chain D: G.516, D.517, M.518, Q.519 Ligand excluded by PLIP SO4.77: 2 residues within 4Å: Chain D: R.515, G.516 Ligand excluded by PLIP SO4.78: 3 residues within 4Å: Chain D: D.94 Ligands: NAG-NAG-BMA.61, NAG-NAG-BMA.61 Ligand excluded by PLIP SO4.79: 4 residues within 4Å: Chain D: D.225, Y.326, N.457 Ligands: NAG.66 Ligand excluded by PLIP

4 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: 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 PC.40: 12 residues within 4Å: Chain B: D.160, H.162, D.232, H.236, N.272, H.273, H.379, H.411, H.413 Ligands: ZN.27, ZN.28, SO4.29 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.272 Salt bridges: B:H.162, B:H.236, B:H.273, B:H.411, B:H.413 pi-Cation interactions: B:H.413 PC.60: 12 residues within 4Å: Chain C: D.160, H.162, D.232, H.236, N.272, H.273, H.379, H.411, H.413 Ligands: ZN.47, ZN.48, SO4.49 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.272, C:N.272 Salt bridges: C:H.162, C:H.236, C:H.273, C:H.411, C:H.413 pi-Cation interactions: C:H.413 PC.80: 12 residues within 4Å: Chain D: D.160, H.162, D.232, H.236, N.272, H.273, H.379, H.411, H.413 Ligands: ZN.67, ZN.68, SO4.69 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.272, D:N.272 Salt bridges: D:H.162, D:H.236, D:H.273, D:H.411, D:H.413 pi-Cation interactions: D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Sphingomyelin phosphodiesterase

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