SMTL ID : 5ebb.1 (2 other biounits)

Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.12, D.77, N.118, H.219, H.260 Ligands: ZN.2, MLI.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.77, A:H.219, A:H.260 ZN.2: 7 residues within 4Å: Chain A: D.12, H.14, D.77, H.260, H.262 Ligands: ZN.1, MLI.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.12, A:H.14, A:D.77, A:H.262

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

NAG.3: 3 residues within 4Å: Chain A: T.26, G.34, N.36 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.26 Hydrogen bonds: A:N.36 NAG.4: 5 residues within 4Å: Chain A: P.17, Y.52, N.98, T.101, T.102 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.101 Hydrogen bonds: A:Y.52, A:N.98 NAG.5: 5 residues within 4Å: Chain A: Y.321, N.323, E.326, L.329, S.380 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.299, A:N.323, A:E.326, A:S.380

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

MLI.6: 12 residues within 4Å: Chain A: D.12, H.14, D.77, H.81, N.118, H.119, Y.181, H.219, H.260, H.262 Ligands: ZN.1, ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.181 Salt bridges: A:H.14, A:H.81, A:H.119, A:H.119, A:H.219, A:H.260, A:H.260, A:H.262

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
A

Acid sphingomyelinase-like phosphodiesterase 3a

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