MolNFT v1 · #189706 · protein
VAS5 spike (3 rbd down)
7VRW · Spike glycoprotein: “VAS5 spike (3 rbd down)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #189706 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VRW
- Type
- protein
- Length
- 3,231 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 21% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 1077 | 21% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.84 | 0.85 | 149 | empty |
| 2 | 678 | 0.82 | 0.87 | 70 | empty |
| 3 | 559 | 0.81 | 0.87 | 45 | empty |
| 4 | 715 | 0.80 | 0.85 | 87 | empty |
| 5 | 699 | 0.80 | 0.84 | 79 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6308 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 6283 Ų buried · 53 hydrogen bonds · protein-protein
- B–A · 6270 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7VRW · VAS5 Spike (3 RBD down) · the same entry in another collection · chain B against B, TM-score 1.00
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 P0DTC2
- Elsewhere: RCSB PDB 7VRW · PDBe 7VRW · UniProt P0DTC2
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