MolNFT v1 · #120308 · protein

Crystal structure of SNX16 px-coiled coil in space group P212121

5GW1 · Sorting nexin-16: “Crystal structure of SNX16 px-coiled coil in space group P212121”. X-ray diffraction, 18 pockets (best druggability 0.82). MolNFT v1 #120308 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GW1
Type: protein
Length: 1,381 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorting nexin-16
UniProt: P57768
Pockets: 18 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sorting nexin-16	protein	175	52% helix, 15% strand	P57768
B	Sorting nexin-16	protein	173	53% helix, 14% strand	P57768
C, E	Sorting nexin-16	protein	176	51% helix, 13% strand	P57768
D	Sorting nexin-16	protein	172	53% helix, 16% strand	P57768
F	Sorting nexin-16	protein	171	47% helix, 14% strand	P57768
G	Sorting nexin-16	protein	165	51% helix, 10% strand	P57768
H	Sorting nexin-16	protein	173	53% helix, 16% strand	P57768

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	950	0.82	0.83	93	empty
2	938	0.82	0.83	80	empty
3	537	0.78	0.84	41	empty
4	213	0.76	0.91	34	empty
5	463	0.75	0.84	56	empty

Interfaces

10 interfaces between chains.

A–B · 1885 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 1741 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1682 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 1578 Å² buried · 5 hydrogen bonds · protein-protein
D–H · 599 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

5GW1 · Crystal structure of SNX16 PX-Coiled coil in space group P212121 · the same entry in another collection · chain H against H, TM-score 1.00
P57768 · AlphaFold monomer V2.0 prediction for sorting nexin-16 (P57768) · a predicted model of the same protein · chain H against A, TM-score 0.74

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 5GW1 · PDBe 5GW1 · UniProt P57768

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