Research workbench
SARS-cov-2 spike in complex with the S2H13 neutralizing antibody Fab fragment (local refinement of the receptor-binding motif and Fab variable domains)
Analyse SARS-cov-2 spike in complex with the S2H13 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
- 7JV2
- Type
- protein
- Length
- 282 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2H13 Fab heavy chain; S2H13 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 4 · best druggability 0.47
Structure
electron microscopy · 3 distinct chains · 3% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S2H13 Fab heavy chain | protein | 119 | 3% helix, 49% strand | — |
| L | S2H13 Fab light chain | protein | 110 | 5% helix, 43% strand | — |
| A | Spike glycoprotein | protein | 53 | 0% helix, 25% strand | P0DTC2 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.47 | 0.78 | 19 | empty |
| 2 | 80 | 0.35 | 0.76 | 17 | empty |
| 3 | 81 | 0.33 | 0.75 | 23 | empty |
| 4 | 72 | 0.30 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 987 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 434 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 341 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7JV2 · SARS-CoV-2 spike in complex with the S2H13 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 7JV2 · PDBe 7JV2 · UniProt P0DTC2
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