Research workbench
SARS-CoV-2 spike in complex with the Ab4 neutralizing antibody (State 3)
Analyse SARS-CoV-2 spike in complex with the Ab4 neutralizing antibody (State 3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E39
- Type
- protein
- Length
- 414 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike protein S1; Light Chain of Ab4; Heavy Chain of Ab4
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.70
Structure
electron microscopy · resolution 3.7 · 3 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 16% helix, 24% strand | P0DTC2 |
| B | Light Chain of Ab4 | protein | 106 | 3% helix, 50% strand | — |
| C | Heavy Chain of Ab4 | protein | 114 | 0% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.70 | 0.88 | 39 | empty |
| 2 | 92 | 0.67 | 0.92 | 29 | empty |
| 3 | 79 | 0.33 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 753 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 284 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7E39 · SARS-cov-2 spike in complex with the AB4 neutralizing antibody (state 3) · 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 7E39 · PDBe 7E39 · UniProt P0DTC2
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