SMTL ID : 6g7o.1

Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: S.77, H.81, H.217, W.220, H.221 Ligands: OLB.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.81, A:H.217, A:H.221, H2O.1

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

SO4.2: 4 residues within 4Å: Chain A: E.60, K.61, R.62 Ligands: MG.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.61, A:R.62 Salt bridges: A:K.61, A:R.62 SO4.3: 3 residues within 4Å: Chain A: K.259, K.339, R.342 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.259, A:K.339 Salt bridges: A:K.259, A:K.339, A:R.342 SO4.4: 4 residues within 4Å: Chain A: F.108, F.111, R.159, Y.162 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.159 SO4.5: 1 residues within 4Å: Chain A: Y.119 No protein-ligand interaction detected (PLIP) SO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.7: 4 residues within 4Å: Chain A: D.265, N.266, A.267 Ligands: MG.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.267

3 x NA: SODIUM ION(Non-functional Binders)

NA.8: 1 residues within 4Å: Chain A: W.219 No protein-ligand interaction detected (PLIP) NA.9: 2 residues within 4Å: Chain A: D.246, E.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.246 NA.10: 3 residues within 4Å: Chain A: T.14, D.19, N.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.14, A:T.14, A:D.19, A:N.24

1 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.11: 22 residues within 4Å: Chain A: W.20, M.43, L.70, V.73, D.92, E.93, M.96, S.99, F.103, H.145, Q.146, Y.149, L.156, F.182, F.186, W.189, W.220, H.221, T.224, S.228, H.231 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.20, A:L.70, A:F.103, A:F.103, A:Y.149, A:L.156, A:F.182, A:H.231 Hydrogen bonds: A:W.189 Salt bridges: A:H.145

1 x CA: CALCIUM ION(Non-covalent)

CA.12: 6 residues within 4Å: Chain A: R.7, D.19, W.20, E.22, N.24, E.33 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.19, A:D.19, A:W.20, A:E.22, A:E.33

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.13: 1 residues within 4Å: Ligands: SO4.7 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: E.60, K.114, N.115 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vasiliauskaite-Brooks, I. et al., Structure of a human intramembrane ceramidase explains enzymatic dysfunction found in leukodystrophy. Nat Commun (2018)

Release Date

2019-01-02

Peptides

Alkaline ceramidase 3,Soluble cytochrome b562: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Alkaline ceramidase 3,Soluble cytochrome b562

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