Research workbench
G32A4 Fab in complex with SARS-cov-2 spike 6P (rbd local reconstruction)
Analyse G32A4 Fab in complex with SARS-cov-2 spike 6P (rbd local reconstruction) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SWN
- Type
- protein
- Length
- 422 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; G32A4 Fab heavy chain; G32A4 Fab light chain
- UniProt
- P0DTC2
- Pockets
- 7 · best druggability 0.70
Structure
electron microscopy · 3 distinct chains · 7% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 11% helix, 16% strand | P0DTC2 |
| H | G32A4 Fab heavy chain | protein | 120 | 8% helix, 46% strand | — |
| L | G32A4 Fab light chain | protein | 108 | 0% helix, 39% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.70 | 0.96 | 22 | empty |
| 2 | 52 | 0.65 | 0.94 | 17 | empty |
| 3 | 141 | 0.53 | 0.81 | 29 | empty |
| 4 | 149 | 0.41 | 0.74 | 21 | empty |
| 5 | 76 | 0.36 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 836 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 510 Ų buried · 1 hydrogen bond · protein-protein
- A–L · 214 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7SWN · G32A4 Fab in complex with SARS-CoV-2 Spike 6P (RBD local reconstruction) · 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 7SWN · PDBe 7SWN · UniProt P0DTC2
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