Research workbench
SARS-cov-2 spike in complex with the S2A4 neutralizing antibody Fab fragment (local refinement of the receptor-binding domain and Fab variable domains)
Analyse SARS-cov-2 spike in complex with the S2A4 neutralizing antibody Fab fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JVA
- Type
- protein
- Length
- 420 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2A4 Fab heavy chain; S2A4 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 4 · best druggability 0.57
Structure
electron microscopy · 3 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S2A4 Fab heavy chain | protein | 117 | 8% helix, 53% strand | — |
| L | S2A4 Fab light chain | protein | 110 | 5% helix, 44% strand | — |
| A | Spike glycoprotein | protein | 193 | 13% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, H
- BMA · beta-D-mannopyranose · sugar · chains H
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 | 197 | 0.57 | 0.80 | 24 | empty |
| 2 | 128 | 0.48 | 0.79 | 30 | empty |
| 3 | 138 | 0.40 | 0.74 | 25 | empty |
| 4 | 79 | 0.36 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 832 Ų buried · 7 hydrogen bonds · protein-protein
- L–A · 511 Ų buried · 8 hydrogen bonds · protein-protein
- H–A · 415 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7JVA · SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment (local… · 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
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7JVA · PDBe 7JVA · UniProt P0DTC2
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