SMTL ID : 2zxc.2 (1 other biounit)

Ceramidase complexed with C2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.97, H.204, E.411, Y.441, Y.448 Ligands: 2ED.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.97, A:H.204, A:E.411, A:Y.448, H2O.1

1 x 2ED: N-[(1R,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]acetamide(Non-covalent)

2ED.2: 16 residues within 4Å: Chain A: G.25, Y.26, S.27, R.160, H.204, S.334, T.335, E.336, D.337, G.338, P.339, G.340, P.341, Y.448, Y.460 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.335, A:P.341, A:Y.460, A:Y.460 Hydrogen bonds: A:D.337, A:G.338, A:G.338, A:Y.460, A:Y.460

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: F.67, Q.68, S.106, Y.108, A.444, Y.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.68, A:S.106, A:Y.445 Water bridges: A:H.107 FMT.4: 1 residues within 4Å: Chain A: V.231 No protein-ligand interaction detected (PLIP) FMT.5: 4 residues within 4Å: Chain A: V.85, D.87, N.89, N.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.85, A:N.89 FMT.6: 1 residues within 4Å: Chain A: Y.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.281 Water bridges: A:L.194

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 4 residues within 4Å: Chain A: R.55, Y.82, V.85, Q.138 No protein-ligand interaction detected (PLIP) DMS.8: 4 residues within 4Å: Chain A: E.88, N.89, F.299, S.495 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.495 Salt bridges: A:E.88

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 7 residues within 4Å: Chain A: H.37, T.578, D.579, N.580, D.581, T.584, Q.585 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.37, A:D.581, A:T.584, A:T.584, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inoue, T. et al., Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase. J.Biol.Chem. (2009)

Release Date

2009-02-03

Peptides

Neutral ceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Neutral ceramidase

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