MolNFT v1 · #129905 · protein
VSV G CR3
5OY9 · Glycoprotein G: “VSV G CR3”. X-ray diffraction, 2 ligands (NAG, CA), 6 pockets (best druggability 0.69). MolNFT v1 #129905 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OY9
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G; Low-density lipoprotein receptor
- UniProt
- P0C2X0, P01130
- Ligands
- NAG, CA
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein G | protein | 410 | 16% helix, 36% strand | P0C2X0 |
| D | Low-density lipoprotein receptor | protein | 37 | 8% helix, 16% strand | P01130 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.69 | 0.97 | 16 | empty |
| 2 | 108 | 0.57 | 0.85 | 19 | empty |
| 3 | 146 | 0.43 | 0.75 | 31 | empty |
| 4 | 84 | 0.37 | 0.76 | 14 | empty |
| 5 | 95 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 772 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, methylation).
Compared structures
- P01130 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor (P01130) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 P0C2X0
- Every structure of UniProt P01130
- Elsewhere: RCSB PDB 5OY9 · PDBe 5OY9 · UniProt P0C2X0 · UniProt P01130
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