MolNFT v1 · #189239 · protein
Cryo-EM structure of SARS-cov-2 S-gamma variant (P.1), two rbd-up conformation
7V7A · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 S-gamma variant (P.1), two rbd-up conformation”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #189239 on GenesisL1: 3D structure…
- PDB
- 7V7A
- Type
- protein
- Length
- 3,119 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1038 | 20% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1043 | 22% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 85 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.87 | 0.88 | 136 | empty |
| 2 | 1003 | 0.84 | 0.85 | 95 | empty |
| 3 | 821 | 0.82 | 0.84 | 60 | empty |
| 4 | 1126 | 0.79 | 0.80 | 96 | empty |
| 5 | 822 | 0.73 | 0.78 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4318 Ų buried · 39 hydrogen bonds · protein-protein
- C–B · 3970 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 3967 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7V7A · Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1), two RBD-up conformation · 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 7V7A · PDBe 7V7A · UniProt P0DTC2
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