Research workbench
Rbd-1 of SARS-cov-2 beta spike in complex with S5D2 Fab
Analyse Rbd-1 of SARS-cov-2 beta spike in complex with S5D2 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WCR
- Type
- protein
- Length
- 628 residues
- Chains
- 3
- 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
- 6 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 197 | 8% helix, 19% strand | P0DTC2 |
| a | Heavy chain of S5D2 Fab | protein | 214 | 1% helix, 51% strand | — |
| b | Light chain of S5D2 Fab | protein | 217 | 6% helix, 49% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.72 | 0.98 | 19 | empty |
| 2 | 222 | 0.48 | 0.75 | 34 | empty |
| 3 | 145 | 0.44 | 0.76 | 26 | empty |
| 4 | 104 | 0.42 | 0.78 | 25 | empty |
| 5 | 125 | 0.40 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- a–b · 1884 Ų buried · 9 hydrogen bonds · protein-protein
- A–b · 346 Ų buried · 2 hydrogen bonds · protein-protein
- A–a · 345 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7WCR · RBD-1 of SARS-CoV-2 Beta spike in complex with 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 7WCR · PDBe 7WCR · UniProt P0DTC2
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