MolNFT v1 · #190061 · protein
SARS-cov-2 beta spike in complex with two S3H3 fabs
7WDF · Spike glycoprotein: “SARS-cov-2 beta spike in complex with two S3H3 fabs”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #190061 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7WDF
- Type
- protein
- Length
- 4,101 residues
- Chains
- 7
- 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, B, C | Spike glycoprotein | protein | 1079 | 20% helix, 30% strand | P0DTC2 |
| D, F | Heavy chain of S3H3 Fab | protein | 217 | 5% helix, 56% strand | — |
| E, G | Light chain of S3H3 Fab | protein | 215 | 7% helix, 53% 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 | 644 | 0.84 | 0.88 | 91 | empty |
| 2 | 761 | 0.84 | 0.87 | 79 | empty |
| 3 | 641 | 0.80 | 0.85 | 62 | empty |
| 4 | 697 | 0.79 | 0.83 | 62 | empty |
| 5 | 667 | 0.77 | 0.83 | 51 | empty |
Interfaces
9 interfaces between chains.
- B–C · 5319 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 5114 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 5098 Ų buried · 47 hydrogen bonds · protein-protein
- D–E · 1765 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1728 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide (disulfide).
Compared structures
- 7WDF · SARS-CoV-2 Beta spike in complex with two S3H3 Fabs · the same entry in another collection · chain D against D, 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 7WDF · PDBe 7WDF · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.