MolNFT v1 · #178087 · protein
Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 Fab (STATE1, local refinement of the rbd, ntd and 35B5 Fab)
7F46 · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 Fab (STATE1, local refinement of the rbd, ntd…”. Electron microscopy, 1 ligand (NAG), 11 pockets (best druggability 0.73). MolNFT v1 #178087 on…
- PDB
- 7F46
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of 35B5 Fab; Light chain of 35B5 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.73
Structure
electron microscopy · 4 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 203 | 0% helix, 48% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 195 | 14% helix, 22% strand | P0DTC2 |
| H | Heavy chain of 35B5 Fab | protein | 226 | 3% helix, 46% strand | — |
| L | Light chain of 35B5 Fab | protein | 218 | 1% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.73 | 0.76 | 71 | empty |
| 2 | 105 | 0.52 | 0.81 | 17 | empty |
| 3 | 233 | 0.50 | 0.75 | 33 | empty |
| 4 | 214 | 0.46 | 0.74 | 31 | empty |
| 5 | 54 | 0.44 | 0.84 | 17 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1676 Ų buried · 5 hydrogen bonds · protein-protein
- B–H · 496 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 237 Ų buried · 0 hydrogen bonds · protein-protein
- C–H · 152 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7F46 · Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab (state1, local… · the same entry in another collection · chain C against C, 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 7F46 · PDBe 7F46 · UniProt P0DTC2
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