SMTL ID : 5u84.1 (1 other biounit)

Acid ceramidase (ASAH1, aCDase) from common minke whale, Cys143Ala, uncleaved

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

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

NAG-NAG-FUC.1: 3 residues within 4Å: Chain A: N.162, N.163, V.166 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: 9 residues within 4Å: Chain A: P.98, G.99, P.100, F.101, R.243, S.244, E.247, N.248 Ligands: IOD.27 No protein-ligand interaction detected (PLIP)

7 x I3C: 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid(Non-functional Binders)(Non-covalent)

I3C.3: 1 residues within 4Å: Ligands: IOD.20 No protein-ligand interaction detected (PLIP) I3C.4: 5 residues within 4Å: Chain A: S.339, F.340, A.341, K.367, Q.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.340, A:K.367 Salt bridges: A:K.367 pi-Cation interactions: A:K.367 I3C.5: 6 residues within 4Å: Chain A: Y.25, P.26, P.27, Y.32, E.371, Y.373 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.26 Hydrogen bonds: A:Y.373 Halogen bonds: A:Y.32 I3C.6: 6 residues within 4Å: Chain A: Y.48, K.49, H.52, G.107, A.110, V.111 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.107 Salt bridges: A:K.49, A:H.52 pi-Stacking: A:H.52 Halogen bonds: A:Y.48 I3C.7: 4 residues within 4Å: Chain A: R.182, N.183, S.184, K.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.183 Salt bridges: A:R.182, A:K.185 Halogen bonds: A:R.182 I3C.8: 4 residues within 4Å: Chain A: H.52, V.56, D.57, V.111 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.57 Water bridges: A:H.52, A:H.52, A:A.59, A:A.59 Salt bridges: A:H.52 Halogen bonds: A:D.57, A:V.111 I3C.9: 13 residues within 4Å: Chain A: N.123, I.124, E.127, F.128, L.212, V.225, I.241, I.242, I.264, L.265, A.266, A.268, F.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.127, A:I.241, A:L.265, A:A.266

18 x IOD: IODIDE ION(Non-functional Binders)

IOD.10: 3 residues within 4Å: Chain A: D.286, R.287, V.288 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: T.324, K.327, M.328, N.331 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: Y.25, P.26, A.341 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: D.44, L.45 Ligand excluded by PLIP IOD.14: 6 residues within 4Å: Chain A: Y.304, V.305, V.306, R.312, R.323, K.327 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain A: Y.68, N.71, N.161, N.163 Ligand excluded by PLIP IOD.16: 6 residues within 4Å: Chain A: T.308, Y.310, D.320, N.321, R.322, R.323 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: I.258, K.261 Ligands: IOD.26 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain A: P.35 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: T.324, P.325, M.328 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Ligands: I3C.3 Ligand excluded by PLIP IOD.21: 4 residues within 4Å: Chain A: R.21, T.349, K.350 Ligands: IOD.24 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain A: P.47, G.99, P.100, E.103 Ligand excluded by PLIP IOD.23: 3 residues within 4Å: Chain A: T.333, N.337, T.342 Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain A: D.19, R.21 Ligands: IOD.21 Ligand excluded by PLIP IOD.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.26: 4 residues within 4Å: Chain A: K.261, S.262, K.263 Ligands: IOD.17 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain A: L.43, R.50 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by 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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Acid ceramidase

Related Entries With Identical Sequence