Research workbench
SARS-cov-2 omicron spike protein SD1 in complex with S3H3 Fab
Analyse SARS-cov-2 omicron spike protein SD1 in complex with S3H3 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WK8
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of S3H3 Fab; Light chain of S3H3 Fab; Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 6 · best druggability 0.61
Structure
electron microscopy · 4 distinct chains · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Heavy chain of S3H3 Fab | protein | 217 | 1% helix, 53% strand | — |
| D | Light chain of S3H3 Fab | protein | 215 | 4% helix, 48% strand | — |
| B | Spike glycoprotein | protein | 18 | 0% helix, 22% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 66 | 0% helix, 41% strand | P0DTC2 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.61 | 0.76 | 50 | empty |
| 2 | 335 | 0.52 | 0.73 | 49 | empty |
| 3 | 56 | 0.50 | 0.87 | 18 | empty |
| 4 | 72 | 0.47 | 0.82 | 24 | empty |
| 5 | 65 | 0.32 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1857 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 918 Ų buried · 14 hydrogen bonds · protein-protein
- C–A · 516 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 334 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 125 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7WK8 · SARS-CoV-2 Omicron spike protein SD1 in complex with S3H3 Fab · the same entry in another collection · chain C against C, 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 7WK8 · PDBe 7WK8 · UniProt P0DTC2
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