Research workbench
SARS-cov-2 spike in complex with the S2A4 neutralizing antibody Fab fragment
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
- 7JVC
- Type
- protein
- Length
- 4,272 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2A4 Fab heavy chain; S2A4 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 990 | 21% helix, 35% strand | P0DTC2 |
| H, C, F | S2A4 Fab heavy chain | protein | 220 | 10% helix, 50% strand | — |
| L, D, G | S2A4 Fab light chain | protein | 214 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, B, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains H, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.86 | 0.87 | 150 | empty |
| 2 | 1150 | 0.85 | 0.86 | 141 | empty |
| 3 | 1083 | 0.83 | 0.84 | 125 | empty |
| 4 | 975 | 0.81 | 0.83 | 117 | empty |
| 5 | 586 | 0.80 | 0.86 | 93 | empty |
Interfaces
12 interfaces between chains.
- A–E · 4293 Ų buried · 31 hydrogen bonds · protein-protein
- B–E · 4283 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 4277 Ų buried · 31 hydrogen bonds · protein-protein
- H–L · 801 Ų buried · 0 hydrogen bonds · protein-protein
- F–G · 779 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7JVC · SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment · 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 7JVC · PDBe 7JVC · UniProt P0DTC2
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