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

Open form of murine Acid Sphingomyelinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

2 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.1: 4 residues within 4Å: Chain A: T.98, W.99, N.100, K.366 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.366 NAG-NAG-FUC.2: 11 residues within 4Å: Chain A: H.61, L.62, D.65, D.66, Q.212, S.213, R.214, T.247, P.248, N.260, Q.261 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.62 Hydrogen bonds: A:D.65, A:D.66, A:N.260, A:R.214

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-FUC.3: 14 residues within 4Å: Chain A: D.94, W.99, N.100, I.101, S.102, F.256, N.320, T.322, D.323, P.324, A.325, G.326, Q.329, E.333 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.256 Hydrogen bonds: A:Q.329

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.4: 8 residues within 4Å: Chain A: I.443, N.445, T.447, Q.448, K.459, L.461, F.497, G.502 No protein-ligand interaction detected (PLIP)

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.5: 4 residues within 4Å: Chain A: N.11, C.14, P.15, K.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.18

3 x ZN: ZINC ION(Non-covalent)

ZN.6: 7 residues within 4Å: Chain A: D.131, H.133, D.203, H.350, H.382, H.384 Ligands: ZN.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:H.133, A:D.203, A:H.384, H2O.1 ZN.7: 7 residues within 4Å: Chain A: D.131, D.203, N.243, H.244, H.350, H.382 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.203, A:H.350, A:H.382, H2O.1 ZN.8: 2 residues within 4Å: Chain A: H.5, H.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.5, A:H.7, H2O.1

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

SO4.9: 3 residues within 4Å: Chain A: E.313, H.355, H.382 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.355, A:H.382 SO4.10: 1 residues within 4Å: Chain A: K.230 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.230 SO4.11: 6 residues within 4Å: Chain A: V.123, Q.424, L.437, D.438, R.463, R.465 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.424, A:D.438, A:R.465 SO4.12: 6 residues within 4Å: Chain A: P.508, C.509, G.510, T.511, P.512, C.513 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.508, A:G.510, A:C.513 SO4.13: 8 residues within 4Å: Chain A: W.362, L.397, R.525, D.527, S.528, P.529, A.530, L.531 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.530 Salt bridges: A:R.525 SO4.14: 2 residues within 4Å: Chain A: V.40, K.43 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.43 SO4.15: 3 residues within 4Å: Chain A: R.460, R.463, E.466 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.460, A:R.463 SO4.16: 8 residues within 4Å: Chain A: L.139, T.142, R.153, R.154, G.155, S.156, G.157, W.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.155, A:G.157 SO4.17: 6 residues within 4Å: Chain A: L.103, P.104, V.106, P.107, K.108, R.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.104, A:K.108 Salt bridges: A:R.370 SO4.18: 3 residues within 4Å: Chain A: L.85, L.86, G.87 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Crystal structure of mammalian acid sphingomyelinase. Nat Commun (2016)

Release Date

2016-07-06

Peptides

Sphingomyelin phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sphingomyelin phosphodiesterase

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