Research workbench
Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Analyse Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JXC
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.47
- Source
- Homo sapiens
- Molecule
- S2H14 antigen-binding (Fab) fragment
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · resolution 2.47 · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S2H14 antigen-binding (Fab) fragment | protein | 215 | 8% helix, 51% strand | — |
| L | S2H14 antigen-binding (Fab) fragment | protein | 213 | 7% helix, 50% strand | — |
Ligands and binding sites
- 2PE · Nonaethylene glycol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.55 | 0.75 | 38 | 2PE |
| 2 | 265 | 0.51 | 0.75 | 27 | empty |
| 3 | 116 | 0.42 | 0.76 | 21 | empty |
| 4 | 93 | 0.41 | 0.78 | 27 | empty |
| 5 | 95 | 0.40 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- H–L · 1573 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JXC · Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike receptor-binding… · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 7JXC · PDBe 7JXC
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