Research workbench
SARS-CoV-2 Beta spike in complex with two S5D2 Fabs
Analyse SARS-CoV-2 Beta spike in complex with two S5D2 Fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WD0
- Type
- protein
- Length
- 4,099 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Mus musculus; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Heavy chain of S5D2 Fab; Light chain of S5D2 Fab
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.3 · 3 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1079 | 20% helix, 30% strand | P0DTC2 |
| a, c | Heavy chain of S5D2 Fab | protein | 214 | 3% helix, 50% strand | — |
| b, d | Light chain of S5D2 Fab | protein | 217 | 4% helix, 47% strand | — |
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 | 838 | 0.85 | 0.87 | 77 | empty |
| 2 | 469 | 0.82 | 0.90 | 59 | empty |
| 3 | 135 | 0.79 | 0.96 | 31 | empty |
| 4 | 125 | 0.79 | 0.97 | 30 | empty |
| 5 | 108 | 0.78 | 0.98 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4571 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 4566 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 4421 Ų buried · 29 hydrogen bonds · protein-protein
- a–b · 1818 Ų buried · 17 hydrogen bonds · protein-protein
- c–d · 1784 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 7WD0 · SARS-cov-2 beta spike in complex with two S5D2 fabs · 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 7WD0 · PDBe 7WD0 · UniProt P0DTC2
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