SMTL ID : 4wgk.1 (1 other biounit)

Crystal structure of human neutral ceramidase with Zn-bound phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 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: 7 residues within 4Å: Chain A: L.561, Q.562, I.577, H.624, K.625, G.626, N.632 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: N.210, N.211, S.212, D.294, M.295 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.294

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.96, H.205, E.442, Y.481 Ligands: PO4.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.96, A:H.205, A:E.442, A:E.442, A:Y.481

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: L.36, N.613, D.614, A.615, S.616, T.619 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.36, A:S.616, A:T.619, A:T.619, H2O.3

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

NAG.5: 3 residues within 4Å: Chain A: N.342, T.344, H.345 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: N.119, Q.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 10 residues within 4Å: Chain A: G.24, M.64, H.96, H.98, H.205, E.442, Y.478, Y.481, Y.493 Ligands: ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.478, A:Y.478, A:Y.481 Water bridges: A:R.159, A:R.159 Salt bridges: A:H.96, A:H.98

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.8: 9 residues within 4Å: Chain A: N.151, Y.175, S.176, S.177, T.179, D.180, K.181, E.182, R.449 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.151, A:S.176, A:S.177, A:K.181, A:E.182 Salt bridges: A:K.181, A:R.449, A:R.449 CIT.9: 4 residues within 4Å: Chain A: E.458, H.462, R.513, K.517 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.458 Water bridges: A:R.513 Salt bridges: A:H.462, A:R.513, A:R.513, A:R.513, A:K.517, A:K.517

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Airola, M.V. et al., Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase. Structure (2015)

Release Date

2015-07-08

Peptides

Neutral ceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neutral ceramidase

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