Research workbench
SARS-cov-2 omicron closed state spike protein in complex with S3H3 Fab
Analyse SARS-cov-2 omicron closed state spike protein 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
- 7WKA
- Type
- protein
- Length
- 4,017 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of S3H3 Fab; Light chain of S3H3 Fab
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Spike glycoprotein | protein | 1051 | 18% helix, 27% strand | P0DTC2 |
| c, a | Heavy chain of S3H3 Fab | protein | 217 | 0% helix, 50% strand | — |
| d, b | Light chain of S3H3 Fab | protein | 215 | 7% helix, 49% 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 | 805 | 0.87 | 0.89 | 116 | empty |
| 2 | 557 | 0.83 | 0.89 | 51 | empty |
| 3 | 1015 | 0.83 | 0.84 | 103 | empty |
| 4 | 653 | 0.82 | 0.87 | 86 | empty |
| 5 | 553 | 0.82 | 0.88 | 60 | empty |
Interfaces
9 interfaces between chains.
- C–B · 5562 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 5450 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 5254 Ų buried · 42 hydrogen bonds · protein-protein
- c–d · 1849 Ų buried · 16 hydrogen bonds · protein-protein
- a–b · 1815 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide (disulfide).
Compared structures
- 7WKA · SARS-CoV-2 Omicron closed state spike protein in complex with S3H3 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 7WKA · PDBe 7WKA · UniProt P0DTC2
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