SMTL ID : 5fi9.1 (1 other biounit)

Closed form of murine Acid Sphingomyelinase in complex with bisphosphonate inhibitor AbPA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

monomer

Ligands

3 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: 4 residues within 4Å: Chain A: S.213, R.214, Q.215, N.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.214 NAG-NAG.3: 9 residues within 4Å: Chain A: N.417, I.443, N.445, T.447, Q.448, K.459, L.461, F.497, G.502 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.100, I.101, S.102, K.366 Ligands: NAG-NAG-FUC.2 No protein-ligand interaction detected (PLIP)

1 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.2: 14 residues within 4Å: Chain A: W.99, N.100, I.101, P.254, P.255, F.256, N.320, T.322, D.323, P.324, A.325, G.326, Q.329 Ligands: NAG-NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.100, A:D.323 Hydrophobic interactions: A:F.256

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.4: 5 residues within 4Å: Chain A: N.11, N.49, I.50, A.51, P.52 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 8 residues within 4Å: Chain A: D.131, H.133, D.203, H.350, H.382, H.384 Ligands: ZN.7, NT8.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.131, A:H.133, A:D.203, A:H.384 ZN.7: 7 residues within 4Å: Chain A: D.203, N.243, H.244, H.350, H.382 Ligands: ZN.6, NT8.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.203, A:H.350, A:H.382

1 x NT8: (1-azanyl-1-phosphono-decyl)phosphonic acid(Non-covalent)

NT8.8: 19 residues within 4Å: Chain A: D.131, H.133, D.203, H.207, N.243, H.244, H.350, H.382, T.383, H.384, V.385, F.413, I.414, L.416, Y.499, H.500, P.505 Ligands: ZN.6, ZN.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.207, A:N.243, A:N.243, A:H.244, A:H.382

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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