SMTL ID : 5ebe.2 (2 other biounits)

Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with 5' CMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

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.1: 3 residues within 4Å: Chain A: P.18, Y.53, N.99 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: T.27, N.37 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.27 NAG.3: 1 residues within 4Å: Chain A: N.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.231 NAG.4: 5 residues within 4Å: Chain A: Y.322, N.324, E.327, S.381, S.384 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.322, A:N.324

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: D.13, H.15, D.78, H.263 Ligands: ZN.6, RP5.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.13, A:H.15, A:D.78, A:H.263 ZN.6: 6 residues within 4Å: Chain A: D.78, N.119, H.220, H.261 Ligands: ZN.5, RP5.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.78, A:H.220, A:H.261

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: L.415 No protein-ligand interaction detected (PLIP) GOL.8: 1 residues within 4Å: Chain A: R.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.156

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.9: 3 residues within 4Å: Chain A: S.133, K.134, N.137 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.134

1 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)

RP5.10: 11 residues within 4Å: Chain A: H.15, D.78, H.82, N.119, H.120, H.220, L.226, H.261, H.263 Ligands: ZN.5, ZN.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.119 Salt bridges: A:H.15, A:H.82, A:H.120, A:H.261, A:H.261, A:H.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lim, S.M. et al., The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a - an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity. Febs J. (2016)

Release Date

2016-01-20

Peptides

Acid sphingomyelinase-like phosphodiesterase 3a: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Acid sphingomyelinase-like phosphodiesterase 3a

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