SMTL ID : 6mhm.1 (1 other biounit)

Crystal structure of human acid ceramidase in covalent complex with carmofur

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG-NAG.1: 8 residues within 4Å: Chain A: R.33, M.61, V.64 Chain B: N.30, N.31, T.33, E.38, Q.39 No protein-ligand interaction detected (PLIP)

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.2: 6 residues within 4Å: Chain A: G.99, P.100, F.101 Chain B: T.113, E.116, N.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.99

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 1 residues within 4Å: Chain A: K.89 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.89 SO4.4: 2 residues within 4Å: Chain A: F.129 Chain B: S.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.86 SO4.5: 3 residues within 4Å: Chain A: Q.84, D.87, E.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.87, A:E.88 SO4.8: 5 residues within 4Å: Chain B: S.86, I.87, G.89, D.155, R.156 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.86, B:G.89, B:G.89, B:R.156 Water bridges: B:D.155, B:D.155 Salt bridges: B:R.156 SO4.9: 4 residues within 4Å: Chain B: K.101, D.103, K.132, K.157 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.103 Salt bridges: B:K.101, B:K.132, B:K.157 SO4.10: 3 residues within 4Å: Chain B: E.96, R.156, K.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.96 Salt bridges: B:R.156, B:K.157

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

NAG.6: 5 residues within 4Å: Chain B: G.75, S.120, Y.121, N.144, Q.145 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.121

1 x JRY: hexylcarbamic acid(Covalent)

JRY.7: 8 residues within 4Å: Chain B: C.1, M.19, D.20, F.21, L.69, N.82, E.83, N.178 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.21, B:L.69 Hydrogen bonds: B:E.83, B:E.83, B:N.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dementiev, A. et al., Molecular Mechanism of Inhibition of Acid Ceramidase by Carmofur. J. Med. Chem. (2019)

Release Date

2019-01-23

Peptides

Acid ceramidase subunit alpha: A
Acid ceramidase subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acid ceramidase subunit alpha

Acid ceramidase subunit beta

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