Crystal structure of human VPS29 complexed with rapid-derived cyclic peptide rt-L1

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 37% strand (DSSP).

Ligands and binding sites

• 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · 4 copies · chains C, D, E, A, B, F
• O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · chains B
• GOL · Glycerol · additive · 4 copies · chains A, E, B, F
• MLI · Malonate ion · additive · 2 copies · chains A

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

Pockets

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

Interfaces

8 interfaces between chains.

• A–C · 616 Ų buried · 4 hydrogen bonds · protein-protein
• B–D · 603 Ų buried · 4 hydrogen bonds · protein-protein
• A–B · 406 Ų buried · 2 hydrogen bonds · protein-protein
• A–F · 360 Ų buried · 6 hydrogen bonds · protein-protein
• E–F · 331 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent, 1 modified (covalent ligand, oxidation).

Compared structures

• 6XS9 · Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1 · the same entry in another collection · chain C against C, TM-score 1.00
• Q9UBQ0 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 29… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9UBQ0
• Elsewhere: RCSB PDB 6XS9 · PDBe 6XS9 · UniProt Q9UBQ0