SMTL ID : 5ebe.3 (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

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

NAG.1: 2 residues within 4Å: Chain A: T.27, N.37 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.27 NAG.2: 3 residues within 4Å: Chain A: Y.53, N.99, T.102 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.102 Hydrogen bonds: A:Y.53 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: 6 residues within 4Å: Chain A: N.324, T.326, E.327, S.381, Y.382, S.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.384

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: D.78, N.119, H.220, H.261 Ligands: ZN.6, C5P.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.78, A:H.220, A:H.261, C5P.7 ZN.6: 7 residues within 4Å: Chain A: D.13, H.15, D.78, H.220, H.263 Ligands: ZN.5, C5P.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.13, A:H.15, A:D.78, A:H.263, C5P.7

1 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.7: 15 residues within 4Å: Chain A: D.13, H.15, K.34, D.78, H.82, N.119, H.120, H.220, H.261, T.262, H.263, K.291, E.295 Ligands: ZN.5, ZN.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.34, A:K.34, A:D.78, A:T.262, A:E.295 Salt bridges: A:H.15, A:H.82, A:H.120, A:H.220, A:H.261, A:H.263 pi-Stacking: A:H.82

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.8: 1 residues within 4Å: Chain A: S.355 No protein-ligand interaction detected (PLIP) SCN.9: 2 residues within 4Å: Chain A: P.84, Q.125 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.125

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
C

Acid sphingomyelinase-like phosphodiesterase 3a

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