MolNFT v1 · #70775 · protein

Crystal structure of the SNX17 px domain with bound sulphate

3LUI · Sorting nexin-17: “Crystal structure of the SNX17 px domain with bound sulphate”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.53). MolNFT v1 #70775 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3LUI
Type: protein
Length: 319 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorting nexin-17
UniProt: Q15036
Ligands: SO4
Pockets: 6 · best druggability 0.53

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sorting nexin-17	protein	104	52% helix, 23% strand	Q15036
B	Sorting nexin-17	protein	106	50% helix, 21% strand	Q15036
C	Sorting nexin-17	protein	109	48% helix, 21% strand	Q15036

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	309	0.53	0.74	32	SO4
2	330	0.53	0.74	32	SO4
3	224	0.49	0.75	26	SO4
4	145	0.43	0.75	23	empty
5	87	0.32	0.73	13	empty

Interfaces

3 interfaces between chains.

A–C · 399 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 388 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 337 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3LUI · Crystal structure of the SNX17 PX domain with bound sulphate · the same entry in another collection · chain A against A, TM-score 1.00
Q15036 · AlphaFold monomer V2.0 prediction for sorting nexin-17 (Q15036) · a predicted model of the same protein · chain B 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 Q15036
Elsewhere: RCSB PDB 3LUI · PDBe 3LUI · UniProt Q15036

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