SMTL ID : 6yxh.1

Cryogenic human alkaline ceramidase 3 (ACER3) at 2.6 A resolution determined by Serial Crystallography (SSX) using CrystalDirect

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: S.77, H.81, D.92, H.217, H.221 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.81, A:H.217, A:H.221

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

SO4.2: 4 residues within 4Å: Chain A: E.60, K.61, R.62 Ligands: MG.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.60, 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 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.342 Salt bridges: A:K.259, A:K.339, A:R.342 SO4.4: 3 residues within 4Å: Chain A: F.111, R.159, Y.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.162 Water bridges: A:R.159 Salt bridges: A:R.159 SO4.5: 1 residues within 4Å: Chain A: Y.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.119 SO4.6: 1 residues within 4Å: Ligands: MG.11 No protein-ligand interaction detected (PLIP) SO4.7: 2 residues within 4Å: Chain A: N.266, A.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.267

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

NA.8: 1 residues within 4Å: Chain A: D.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.246 NA.9: 2 residues within 4Å: Chain A: D.19, N.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.19, A:N.24

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: D.19, W.20, E.22, N.24, E.33 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.19, A:W.20, A:E.22, A:E.33

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

MG.11: 1 residues within 4Å: Ligands: SO4.6 No protein-ligand interaction detected (PLIP) MG.12: 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

Healey, R.D. et al., An automated platform for structural analysis of membrane proteins through serial crystallography. Cell Rep Methods (2021)

Release Date

2021-05-12

Peptides

Alkaline ceramidase 3: 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

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