Crystal structure of VAC8P bound to NVJ1P

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).

Ligands and binding sites

• PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 2 copies · chains A, C
• B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B

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

Interfaces

3 interfaces between chains.

• C–D · 2119 Ų buried · 50 hydrogen bonds · protein-protein
• A–B · 2115 Ų buried · 38 hydrogen bonds · protein-protein
• A–C · 964 Ų buried · 11 hydrogen bonds · protein-protein

Compared structures

• 5XJG · Crystal structure of Vac8p bound to Nvj1p · the same entry in another collection · chain A against A, TM-score 1.00
• P39968 · AlphaFold monomer V2.0 prediction for vacuolar protein 8 (P39968) · a predicted model of the same protein · chain A against A, TM-score 0.96
• P38881 · AlphaFold monomer V2.0 prediction for nucleus-vacuole junction protein 1 (P38881) · a predicted model of the same protein · chain B against A, TM-score 0.71

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 P39968
• Every structure of UniProt P38881
• Elsewhere: RCSB PDB 5XJG · PDBe 5XJG · UniProt P39968 · UniProt P38881