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Ceramidase complexed with C2

Analyse Ceramidase complexed with C2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZXC
Type: protein
Length: 1,286 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neutral ceramidase
EC: 3.5.1.23
UniProt: Q9I596
Ligands: 2ED, ZN, MG
Pockets: 10 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Neutral ceramidase (EC 3.5.1.23)	protein	643	23% helix, 31% strand	Q9I596

Ligands and binding sites

2ED · N-[(1R,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]acetamide · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
FMT · Formic acid · additive · 8 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 2 copies · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	138	0.80	0.97	33	2ED
2	240	0.79	0.92	43	2ED
3	812	0.74	0.79	69	empty
4	78	0.52	0.85	16	empty
5	75	0.51	0.84	15	empty

Interfaces

1 interface between chains.

A–B · 303 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2ZXC · Ceramidase complexed with C2 · the same entry in another collection · chain A against A, TM-score 1.00
Q9I596 · AlphaFold monomer V2.0 prediction for neutral ceramidase (Q9I596) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9I596
Elsewhere: RCSB PDB 2ZXC · PDBe 2ZXC · UniProt Q9I596

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