Research workbench

Crystal structure of SNX16 px-coiled coil

Analyse Crystal structure of SNX16 px-coiled coil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GW0
Type: protein
Length: 1,025 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorting nexin-16
UniProt: P57768
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 57% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Sorting nexin-16	protein	173	56% helix, 17% strand	P57768
B	Sorting nexin-16	protein	170	56% helix, 14% strand	P57768
D	Sorting nexin-16	protein	170	57% helix, 15% strand	P57768
E	Sorting nexin-16	protein	171	57% helix, 14% strand	P57768
F	Sorting nexin-16	protein	168	57% helix, 13% strand	P57768

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.79	0.84	58	empty
2	302	0.78	0.90	32	empty
3	625	0.77	0.82	42	empty
4	1090	0.73	0.76	61	empty
5	581	0.73	0.81	45	empty

Interfaces

8 interfaces between chains.

C–E · 1865 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 1830 Å² buried · 7 hydrogen bonds · protein-protein
A–F · 1793 Å² buried · 10 hydrogen bonds · protein-protein
B–F · 365 Å² buried · 2 hydrogen bonds · protein-protein
D–E · 333 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

5GW0 · Crystal structure of SNX16 PX-Coiled coil · the same entry in another collection · chain F against F, TM-score 1.00
P57768 · AlphaFold monomer V2.0 prediction for sorting nexin-16 (P57768) · a predicted model of the same protein · chain D against A, TM-score 0.75

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 P57768
Elsewhere: RCSB PDB 5GW0 · PDBe 5GW0 · UniProt P57768

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.