SMTL ID : 6mhm.2 (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: 9 residues within 4Å: Chain A: R.33, M.61 Chain B: N.30, N.31, T.33, E.38, Q.39, P.42, D.245 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.61, A:M.61

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

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

SO4.3: 3 residues within 4Å: Chain A: G.95, N.96 Chain B: K.102 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.96 Salt bridges: B:K.102 SO4.4: 4 residues within 4Å: Chain A: F.129 Chain B: F.85, S.86, G.89 No protein-ligand interaction detected (PLIP) SO4.5: 3 residues within 4Å: Chain A: Q.84, D.87, E.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.87, A:D.87, A:E.88 SO4.9: 5 residues within 4Å: Chain B: R.84, S.86, D.155, L.160 Ligands: SO4.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.155 Salt bridges: B:R.84 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 SO4.11: 3 residues within 4Å: Chain B: D.103, K.132, K.157 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.132, B:K.157 SO4.12: 6 residues within 4Å: Chain B: S.86, N.88, G.89, D.155, R.156 Ligands: SO4.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.86, B:N.88, B:G.89 Salt bridges: B:R.156

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

NAG.6: 4 residues within 4Å: Chain B: G.75, T.119, S.120, N.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.144 NAG.7: 5 residues within 4Å: Chain B: Y.173, T.193, K.196, M.197, N.200 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.196, B:M.197 Hydrogen bonds: B:N.200

1 x JRY: hexylcarbamic acid(Covalent)

JRY.8: 6 residues within 4Å: Chain B: C.1, M.19, D.20, F.21, E.83, N.178 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.21 Hydrogen bonds: B:C.1, 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
C

B
D

Acid ceramidase subunit alpha

Acid ceramidase subunit beta

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