Research workbench
SARS-cov-2 beta spike in complex with one S5D2 Fab
Analyse SARS-cov-2 beta spike in complex with one S5D2 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WCZ
- Type
- protein
- Length
- 3,668 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of S5D2 Fab; Light chain of S5D2 Fab
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1079 | 20% helix, 30% strand | P0DTC2 |
| a | Heavy chain of S5D2 Fab | protein | 214 | 3% helix, 50% strand | — |
| b | 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 | 989 | 0.88 | 0.89 | 112 | empty |
| 2 | 602 | 0.84 | 0.89 | 78 | empty |
| 3 | 113 | 0.79 | 0.98 | 27 | empty |
| 4 | 966 | 0.79 | 0.81 | 85 | empty |
| 5 | 118 | 0.78 | 0.97 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4651 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 4613 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4374 Ų buried · 28 hydrogen bonds · protein-protein
- a–b · 1819 Ų buried · 17 hydrogen bonds · protein-protein
- A–a · 373 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
- 7WCZ · SARS-CoV-2 Beta spike in complex with one S5D2 Fab · 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 7WCZ · PDBe 7WCZ · UniProt P0DTC2
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