SMTL ID : 5u81.2 (1 other biounit)

Acid ceramidase (ASAH1, aCDase) from naked mole rat, Cys143Ala, uncleaved

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 16 residues within 4Å: Chain A: R.33, D.57, K.58, P.60, M.61, I.64, N.159, N.161, N.162, T.164, E.169, E.170, K.172, P.173, D.376 Ligands: CL.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.61 Hydrophobic interactions: A:N.161 Hydrogen bonds: A:N.159, A:R.33 NAG-NAG-BMA-MAN-MAN-FUC.10: 16 residues within 4Å: Chain B: R.33, D.57, K.58, P.60, M.61, I.64, N.159, N.161, N.162, T.164, E.169, E.170, K.172, P.173, D.376 Ligands: CL.15 2 PLIP interactions: 2 interactions with chain B Water bridges: B:M.61 Hydrophobic interactions: B:N.161 Hydrogen bonds: B:N.159, B:R.33, B:E.170

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 15 residues within 4Å: Chain A: L.43, D.44, L.45, P.46, P.47, R.50, G.99, P.100, Y.101, R.182, R.243, S.244, E.247, N.248 Ligands: PG4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.44, A:L.45, A:R.50 Water bridges: A:D.44 NAG-NAG-BMA-MAN-MAN.11: 15 residues within 4Å: Chain B: L.43, D.44, L.45, P.46, P.47, R.50, G.99, P.100, Y.101, R.182, R.243, S.244, E.247, N.248 Ligands: PG4.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.44, B:L.45, B:R.50

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

NAG-NAG.3: 8 residues within 4Å: Chain A: G.206, Q.207, T.250, S.251, Y.252, N.275, Q.276, T.366 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 8 residues within 4Å: Chain B: G.206, Q.207, T.250, S.251, Y.252, N.275, Q.276, T.366 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: H.143, L.145, S.339, F.340, D.364, K.367, H.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.340, A:D.364, A:H.369 GOL.5: 5 residues within 4Å: Chain A: S.337, L.338, S.339, A.341, T.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.339 Water bridges: A:L.338 GOL.13: 7 residues within 4Å: Chain B: H.143, L.145, S.339, F.340, D.364, K.367, H.369 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.340, B:D.364, B:D.364, B:H.369 GOL.14: 5 residues within 4Å: Chain B: S.337, L.338, S.339, A.341, T.342 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.339 Water bridges: B:L.338

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 6 residues within 4Å: Chain A: R.33, K.172, P.173, L.374 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1, NAG-NAG-BMA-MAN-MAN-FUC.1 Ligand excluded by PLIP CL.7: 9 residues within 4Å: Chain A: M.72, I.154, F.155, L.156, G.157, W.165, V.166, I.167, T.168 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain B: R.33, K.172, P.173, L.374 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.10, NAG-NAG-BMA-MAN-MAN-FUC.10 Ligand excluded by PLIP CL.16: 9 residues within 4Å: Chain B: M.72, I.154, F.155, L.156, G.157, W.165, V.166, I.167, T.168 Ligand excluded by PLIP

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 8 residues within 4Å: Chain A: I.241, S.244, V.245, N.248, A.249, E.254, I.258 Ligands: NAG-NAG-BMA-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.248 PG4.17: 8 residues within 4Å: Chain B: I.241, S.244, V.245, N.248, A.249, E.254, I.258 Ligands: NAG-NAG-BMA-MAN-MAN.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.248

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 9 residues within 4Å: Chain A: K.232 Chain B: F.69, V.73, F.76, V.77, F.129, I.154, F.155, L.156 No protein-ligand interaction detected (PLIP) 1PE.18: 9 residues within 4Å: Chain A: F.69, V.73, F.76, V.77, F.129, I.154, F.155, L.156 Chain B: K.232 No protein-ligand interaction detected (PLIP)

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 isoform b: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Acid ceramidase isoform b

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