MolNFT v1 · #118397 · protein

Structure of VPS35 N terminal region

5F0K · Vacuolar protein sorting-associated protein 35: “Structure of VPS35 N terminal region”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #118397 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5F0K
Type: protein
Length: 2,158 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 35
UniProt: Q96QK1
Ligands: SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein 35	protein	433	74% helix, 0% strand	Q96QK1
B	Vacuolar protein sorting-associated protein 35	protein	430	75% helix, 0% strand	Q96QK1
C	Vacuolar protein sorting-associated protein 35	protein	439	74% helix, 0% strand	Q96QK1
D	Vacuolar protein sorting-associated protein 35	protein	433	71% helix, 0% strand	Q96QK1
E	Vacuolar protein sorting-associated protein 35	protein	423	75% helix, 0% strand	Q96QK1

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, E
EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D, E
GOL · Glycerol · additive · 9 copies · chains A, B, E, C, D
PG4 · Tetraethylene glycol · additive · chains C

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	928	0.81	0.83	97	empty
2	1113	0.79	0.81	109	EDO, GOL
3	1187	0.79	0.80	98	EDO
4	535	0.77	0.84	57	empty
5	590	0.76	0.82	61	EDO, GOL

Interfaces

5 interfaces between chains.

A–B · 1306 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1295 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 1292 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 1238 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 1121 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5F0K · Structure of VPS35 N terminal region · the same entry in another collection · chain E against E, TM-score 1.00
Q96QK1 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 35… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q96QK1
Elsewhere: RCSB PDB 5F0K · PDBe 5F0K · UniProt Q96QK1

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