Research workbench
G32Q4 Fab in complex with SARS-cov-2 spike 6P (rbd local reconstruction)
Analyse G32Q4 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
- 7SWP
- Type
- protein
- Length
- 436 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; G32Q4 Fab heavy chain; G32Q4 Fab light chain
- UniProt
- P0DTC2
- Pockets
- 4 · best druggability 0.63
Structure
electron microscopy · 3 distinct chains · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 15% helix, 24% strand | P0DTC2 |
| H | G32Q4 Fab heavy chain | protein | 129 | 9% helix, 46% strand | — |
| L | G32Q4 Fab light chain | protein | 112 | 7% helix, 42% strand | — |
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 | 311 | 0.63 | 0.80 | 39 | empty |
| 2 | 180 | 0.49 | 0.77 | 30 | empty |
| 3 | 158 | 0.46 | 0.76 | 27 | empty |
| 4 | 130 | 0.40 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- H–L · 786 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 706 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 406 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7SWP · G32Q4 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 7SWP · PDBe 7SWP · UniProt P0DTC2
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