MolNFT v1 · #189666 · protein
Cryo-EM structure of the SARS-cov-2 spike protein (2-up rbd) bound to neutralizing nanobodies P86
7VQ0 · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 spike protein (2-up rbd) bound to neutralizing nanobodies P86”. Electron microscopy, 3 ligands (NAG, MAN, FUC), 20 pockets (best druggability 0.86). MolNFT v1 #189666 on…
- PDB
- 7VQ0
- Type
- protein
- Length
- 3,624 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Neutralizing nanobody P86
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1093 | 23% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1091 | 22% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1092 | 21% helix, 30% strand | P0DTC2 |
| D, E, F | Neutralizing nanobody P86 | protein | 116 | 3% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 copies · chains A, F, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, 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 | 931 | 0.86 | 0.87 | 119 | empty |
| 2 | 1019 | 0.83 | 0.84 | 117 | empty |
| 3 | 424 | 0.82 | 0.91 | 46 | empty |
| 4 | 111 | 0.80 | 0.98 | 25 | empty |
| 5 | 338 | 0.79 | 0.89 | 41 | empty |
Interfaces
8 interfaces between chains.
- A–B · 5413 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 4995 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 4843 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1305 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1042 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 41 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7VQ0 · Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing… · the same entry in another collection · chain A against A, 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 7VQ0 · PDBe 7VQ0 · UniProt P0DTC2
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