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Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D

Analyse Structural basis for ion-coordination and the catalytic mechanism of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XX1
Type: protein
Length: 1,140 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sphingomyelinase I
EC: 3.1.4.41
UniProt: Q8I914
Ligands: MG, SO4
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Sphingomyelinase I (EC 3.1.4.41)	protein	285	38% helix, 21% strand	Q8I914

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 23 copies · chains A, B, C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C, D

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

Pockets

6 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	1197	0.86	0.87	122	SO4
2	1084	0.84	0.85	101	SO4
3	76	0.68	0.93	27	empty
4	371	0.66	0.80	45	SO4, EPE
5	57	0.65	0.94	15	empty

Interfaces

4 interfaces between chains.

C–D · 1301 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1196 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 260 Å² buried · 1 hydrogen bond · protein-protein
B–D · 63 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1XX1 · Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D · the same entry in another collection · chain D against D, TM-score 1.00
Q8I914 · AlphaFold monomer V2.0 prediction for dermonecrotic toxin llsictox- ALPHAIII1I (Q8I914) · 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 Q8I914
Elsewhere: RCSB PDB 1XX1 · PDBe 1XX1 · UniProt Q8I914

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