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

Open form of murine Acid Sphingomyelinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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.1: 13 residues within 4Å: Chain A: D.94, W.99, N.100, I.101, F.256, N.320, T.322, D.323, P.324, A.325, G.326, Q.329, E.333 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.256, A:I.101, A:T.322 Hydrogen bonds: A:Q.329, A:E.333, A:Q.329, A:Q.329

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: 10 residues within 4Å: Chain A: N.417, I.443, N.445, T.447, Q.448, K.459, L.461, F.497, G.502 Ligands: SO4.9 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-FUC.3: 7 residues within 4Å: Chain A: N.11, C.14, P.15, K.18, P.78, S.79, S.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.79, A:K.18 Hydrophobic interactions: A:K.18

3 x ZN: ZINC ION(Non-covalent)

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

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

NAG.7: 3 residues within 4Å: Chain A: T.98, W.99, N.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.100

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

SO4.8: 3 residues within 4Å: Chain A: E.313, H.355, H.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.313 Salt bridges: A:H.355, A:H.382 SO4.9: 6 residues within 4Å: Chain A: Y.172, T.447, G.502, H.503 Ligands: NAG-NAG-BMA-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.447, A:G.502 Salt bridges: A:H.503 SO4.10: 6 residues within 4Å: Chain A: P.508, C.509, G.510, T.511, P.512, C.513 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.510, A:C.513 SO4.11: 5 residues within 4Å: Chain A: W.362, R.525, S.528, P.529, A.530 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.525, A:A.530 SO4.12: 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 SO4.13: 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:V.106, A:K.108 Salt bridges: A:R.370 SO4.14: 5 residues within 4Å: Chain A: G.83, L.84, L.85, L.86, G.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.85, A:G.87

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
B

Sphingomyelin phosphodiesterase

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