Research workbench
Crystal structure of human VPS29 complexed with rapid-derived cyclic peptide rt-D1
Analyse Crystal structure of human VPS29 complexed with rapid-derived cyclic peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XS5
- Type
- protein
- Length
- 199 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 29…
- UniProt
- Q9UBQ0
- Ligands
- 48V
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 29 | protein | 183 | 15% helix, 38% strand | Q9UBQ0 |
| B | 48V-dty-ile-ile-asp-thr-pro-leu-gly-val-phe-leu-ser-ser- leu-lys-arg | protein | 16 | 0% helix, 56% strand | — |
Ligands and binding sites
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · chains B
- GOL · Glycerol · additive · 2 copies · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.46 | 0.84 | 17 | FMT |
| 2 | 50 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 574 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino (covalent ligand, D-amino acid).
Compared structures
- 6XS5 · Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1 · the same entry in another collection · chain A against A, 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 6XS5 · PDBe 6XS5 · UniProt Q9UBQ0
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