MolNFT v1 · #169961 · protein
Crystal structure of human VPS29 complexed with rapid-derived cyclic peptide rt-L2
6XSA · Vacuolar protein sorting-associated protein 29: “Crystal structure of human VPS29 complexed with rapid-derived cyclic peptide rt-L2”. X-ray diffraction, 2 ligands (48V, SO4). MolNFT v1 #169961 on GenesisL1: 3D structure, binding…
- PDB
- 6XSA
- Type
- protein
- Length
- 198 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, SO4
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 38% 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-tyr-leu-pro-thr-ile-thr-gly-val-gly-his-leu-TRP-his- pro-leu | protein | 15 | 0% helix, 33% strand | — |
Ligands and binding sites
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · chains B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XSA · Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L2 · 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 0.99
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 Q9UBQ0
- Elsewhere: RCSB PDB 6XSA · PDBe 6XSA · UniProt Q9UBQ0
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