MolNFT v1 · #59815 · protein

Crystal structure of semet VPS75

3C9B · Vacuolar protein sorting-associated protein 75: “Crystal structure of semet VPS75”. X-ray diffraction, 2 pockets (best druggability 0.58). MolNFT v1 #59815 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3C9B
Type: protein
Length: 397 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 75
UniProt: P53853
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein 75	protein	198	51% helix, 16% strand	P53853
B	Vacuolar protein sorting-associated protein 75	protein	199	51% helix, 16% strand	P53853

Pockets

2 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	216	0.58	0.79	34	empty
2	246	0.56	0.78	34	empty

Interfaces

1 interface between chains.

A–B · 1406 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

3C9B · Crystal structure of SeMet Vps75 · the same entry in another collection · chain A against A, TM-score 1.00
P53853 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 75… · 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 P53853
Elsewhere: RCSB PDB 3C9B · PDBe 3C9B · UniProt P53853

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