MolNFT v1 · #129917 · protein
VSV G CR2
5OYL · Glycoprotein: “VSV G CR2”. X-ray diffraction, 2 ligands (NAG, CA), 6 pockets (best druggability 0.62). MolNFT v1 #129917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OYL
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein; Low-density lipoprotein receptor
- UniProt
- B7UCZ5, P01130
- Ligands
- NAG, CA
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein | protein | 410 | 17% helix, 35% strand | B7UCZ5 |
| D | Low-density lipoprotein receptor | protein | 46 | 13% helix, 13% strand | P01130 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A, D
- GOL · Glycerol · additive · 7 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.62 | 0.85 | 25 | GOL |
| 2 | 135 | 0.57 | 0.83 | 18 | empty |
| 3 | 289 | 0.56 | 0.76 | 37 | empty |
| 4 | 53 | 0.33 | 0.78 | 21 | empty |
| 5 | 72 | 0.32 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–D · 819 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, methylation).
Compared structures
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 B7UCZ5
- Every structure of UniProt P01130
- Elsewhere: RCSB PDB 5OYL · PDBe 5OYL · UniProt B7UCZ5 · UniProt P01130
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.