SMTL ID : 5u7z.3 (2 other biounits)

Human acid ceramidase (ASAH1, aCDase) self-activated

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 12 residues within 4Å: Chain A: R.33, P.60, M.61, V.64, S.68 Chain B: N.30, N.33, T.35, E.40, Q.41, P.44, D.247 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.41, A:R.33

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

SO4.2: 4 residues within 4Å: Chain A: Q.84, D.87, E.88, P.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.84, A:D.87, A:E.88 SO4.3: 3 residues within 4Å: Chain A: G.95, N.96 Chain B: K.104 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.96, A:N.96 Salt bridges: B:K.104 SO4.7: 9 residues within 4Å: Chain B: T.179, N.180, Y.181, P.187, F.188, D.191, D.192, R.193, R.194 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.179, B:N.180, B:D.192, B:R.193, B:R.194 Salt bridges: B:R.193 SO4.8: 3 residues within 4Å: Chain B: R.86, D.157, L.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.157 Salt bridges: B:R.86 SO4.9: 4 residues within 4Å: Chain B: K.103, D.105, K.134, K.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.105 Salt bridges: B:K.103, B:K.134, B:K.159 SO4.10: 8 residues within 4Å: Chain B: R.86, F.87, Y.140, N.180, Y.181, D.182, K.185, F.188 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.140, B:Y.140, B:D.182 Water bridges: B:F.87 Salt bridges: B:R.86, B:K.185

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

NAG.4: 8 residues within 4Å: Chain B: G.77, L.78, T.121, S.122, Y.123, E.124, N.146, Q.147 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.123, B:N.146 NAG.5: 7 residues within 4Å: Chain A: P.100, F.101 Chain B: R.53, R.114, T.115, E.118, N.119 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.118, B:N.119 Hydrophobic interactions: A:P.100 Water bridges: A:R.50 NAG.6: 5 residues within 4Å: Chain B: Y.175, T.195, K.198, M.199, N.202 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.198 Hydrogen bonds: B:N.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gebai, A. et al., Structural basis for the activation of acid ceramidase. Nat Commun (2018)

Release Date

2018-03-28

Peptides

Acid ceramidase: A
Acid ceramidase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Acid ceramidase

Acid ceramidase

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