MolNFT v1 · #182765 · protein
Crystal structure of the SARS-cov-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment C098
7N3I · Spike protein S1: “Crystal structure of the SARS-cov-2 receptor binding domain in complex with the human neutralizing antibody…”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.51). MolNFT v1 #182765 on GenesisL1…
- PDB
- 7N3I
- Type
- protein
- Length
- 622 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; C098 Fab heavy chain; C098 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike protein S1 | protein | 194 | 18% helix, 30% strand | P0DTC2 |
| H | C098 Fab heavy chain | protein | 215 | 8% helix, 51% strand | — |
| L | C098 Fab light chain | protein | 213 | 7% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.51 | 0.80 | 21 | empty |
| 2 | 239 | 0.49 | 0.74 | 35 | empty |
| 3 | 104 | 0.42 | 0.77 | 23 | empty |
| 4 | 104 | 0.34 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1815 Ų buried · 20 hydrogen bonds · protein-protein
- C–H · 798 Ų buried · 18 hydrogen bonds · protein-protein
- C–L · 449 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7N3I · Crystal structure of the SARS-CoV-2 receptor binding domain in complex with the human… · 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 7N3I · PDBe 7N3I · UniProt P0DTC2
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