MolNFT v1 · #190057 · protein
SARS-cov-2 beta spike in complex with three S3H3 fabs
7WD9 · Spike glycoprotein: “SARS-cov-2 beta spike in complex with three S3H3 fabs”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #190057 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7WD9
- Type
- protein
- Length
- 4,533 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of S3H3 Fab; Light chain of S3H3 Fab
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Spike glycoprotein | protein | 1079 | 21% helix, 30% strand | P0DTC2 |
| E, G, I | Heavy chain of S3H3 Fab | protein | 217 | 3% helix, 56% strand | — |
| F, H, J | Light chain of S3H3 Fab | protein | 215 | 7% helix, 51% strand | — |
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 | 855 | 0.84 | 0.86 | 86 | empty |
| 2 | 888 | 0.81 | 0.83 | 76 | empty |
| 3 | 989 | 0.81 | 0.83 | 78 | empty |
| 4 | 664 | 0.80 | 0.85 | 64 | empty |
| 5 | 224 | 0.79 | 0.93 | 43 | empty |
Interfaces
12 interfaces between chains.
- A–B · 5379 Ų buried · 42 hydrogen bonds · protein-protein
- C–B · 5347 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 4809 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 1799 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1774 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide (disulfide).
Compared structures
- 7WD9 · SARS-CoV-2 Beta spike in complex with three S3H3 Fabs · 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 7WD9 · PDBe 7WD9 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.