MolNFT v1 · #187613 · protein
Structure of human SARS-cov-2 neutralizing antibody C1C-A3 Fab
7SN2 · Spike glycoprotein: “Structure of human SARS-cov-2 neutralizing antibody C1C-A3 Fab”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 8 pockets (best druggability 0.63). MolNFT v1 #187613 on GenesisL1: 3D structure, binding sites…
- PDB
- 7SN2
- Type
- protein
- Length
- 650 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Neutralizing antibody C1C-A3 Fab heavy chain; Neutralizing antibody…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 8 · best druggability 0.63
Structure
electron microscopy · 3 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 223 | 13% helix, 15% strand | P0DTC2 |
| H | Neutralizing antibody C1C-A3 Fab heavy chain | protein | 213 | 6% helix, 49% strand | — |
| L | Neutralizing antibody C1C-A3 Fab light chain | protein | 214 | 4% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, L
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains L
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.63 | 0.76 | 52 | empty |
| 2 | 328 | 0.62 | 0.78 | 48 | empty |
| 3 | 76 | 0.54 | 0.87 | 26 | empty |
| 4 | 124 | 0.50 | 0.80 | 28 | empty |
| 5 | 132 | 0.43 | 0.76 | 26 | NAG |
Interfaces
3 interfaces between chains.
- H–L · 1761 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 523 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 438 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7SN2 · Structure of human SARS-CoV-2 neutralizing antibody C1C-A3 Fab · 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 7SN2 · PDBe 7SN2 · UniProt P0DTC2
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