SMTL ID : 5u7z.1 (2 other biounits)

Human acid ceramidase (ASAH1, aCDase) self-activated

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 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: 11 residues within 4Å: Chain A: R.33, P.60, M.61, V.64 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 NAG-NAG-BMA.11: 12 residues within 4Å: Chain C: R.33, P.60, M.61, V.64, S.68 Chain D: N.30, N.33, T.35, E.40, Q.41, P.44, D.247 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.33, D:Q.41

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

SO4.2: 5 residues within 4Å: Chain A: M.83, Q.84, D.87, E.88, P.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.83, A:D.87, A:E.88 SO4.3: 6 residues within 4Å: Chain A: L.43, R.50, P.100 Chain B: R.114, E.118 Ligands: NAG.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.50 Hydrogen bonds: B:E.118 SO4.4: 4 residues within 4Å: Chain A: N.96, E.102, E.103, K.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.103 Salt bridges: A:K.106 SO4.5: 2 residues within 4Å: Chain A: V.85, K.89 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.89 SO4.8: 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 SO4.9: 7 residues within 4Å: Chain B: R.86, S.88, P.138, D.157, L.162 Chain D: K.185 Ligands: SO4.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.157 Salt bridges: B:R.86, D:K.185 SO4.10: 4 residues within 4Å: Chain B: K.103, D.105, K.134, K.159 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.103, B:K.134, B:K.159 SO4.12: 4 residues within 4Å: Chain C: Q.84, D.87, E.88, P.115 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.84, C:D.87, C:E.88 SO4.13: 3 residues within 4Å: Chain C: G.95, N.96 Chain D: K.104 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Salt bridges: D:K.104 Hydrogen bonds: C:N.96, C:N.96 SO4.17: 9 residues within 4Å: Chain D: 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 D Hydrogen bonds: D:T.179, D:N.180, D:D.192, D:R.193, D:R.194 Salt bridges: D:R.193 SO4.18: 5 residues within 4Å: Chain B: K.185 Chain D: R.86, D.157, L.162 Ligands: SO4.9 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.157 Salt bridges: D:R.86, B:K.185 SO4.19: 4 residues within 4Å: Chain D: K.103, D.105, K.134, K.159 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.105 Salt bridges: D:K.103, D:K.134, D:K.159 SO4.20: 8 residues within 4Å: Chain D: R.86, F.87, Y.140, N.180, Y.181, D.182, K.185, F.188 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.140, D:Y.140, D:D.182 Water bridges: D:F.87 Salt bridges: D:R.86, D:K.185

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

NAG.6: 9 residues within 4Å: Chain A: G.99, P.100, F.101 Chain B: R.53, R.114, T.115, E.118, N.119 Ligands: SO4.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.99, B:E.118, B:N.119 NAG.7: 6 residues within 4Å: Chain B: G.77, L.78, S.122, N.146, Q.147, T.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.77, B:Q.147 NAG.14: 8 residues within 4Å: Chain D: G.77, L.78, T.121, S.122, Y.123, E.124, N.146, Q.147 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.123, D:N.146 NAG.15: 7 residues within 4Å: Chain C: P.100, F.101 Chain D: R.53, R.114, T.115, E.118, N.119 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.118, D:N.119 Hydrophobic interactions: C:P.100 Water bridges: C:R.50 NAG.16: 5 residues within 4Å: Chain D: Y.175, T.195, K.198, M.199, N.202 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.198 Hydrogen bonds: D: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: AC
Acid ceramidase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Acid ceramidase

Acid ceramidase

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