Research workbench

Asmase with zinc

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

PDB: 5I8R
Type: protein
Length: 1,584 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sphingomyelin phosphodiesterase
EC: 3.1.4.12
UniProt: P17405
Ligands: NAG, BMA, MAN, ZN
Pockets: 12 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Sphingomyelin phosphodiesterase (EC 3.1.4.12)	protein	528	38% helix, 15% strand	P17405

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B, C
BMA · beta-D-mannopyranose · sugar · 3 copies
MAN · alpha-D-mannopyranose · sugar
ZN · Zinc ion · metal · 6 copies · chains A, B, C

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	853	0.74	0.78	96	empty
2	660	0.74	0.80	74	empty
3	140	0.60	0.84	31	empty
4	203	0.46	0.74	34	empty
5	111	0.38	0.74	21	empty

Interfaces

3 interfaces between chains.

B–C · 672 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 656 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 36 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 13 glycan (disulfide, N-glycosylation).

Compared structures

5I8R · aSMase with zinc · the same entry in another collection · chain A against A, TM-score 1.00
P17405 · AlphaFold monomer V2.0 prediction for sphingomyelin phosphodiesterase (P17405) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P17405
Elsewhere: RCSB PDB 5I8R · PDBe 5I8R · UniProt P17405

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