Research workbench
SARS-cov-2 omicron open state spike protein in complex with S3H3 Fab
Analyse SARS-cov-2 omicron open 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
- 7WK9
- Type
- protein
- Length
- 3,805 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 0.86
Structure
electron microscopy · 6 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1042 | 17% helix, 31% strand | P0DTC2 |
| C, B | Spike glycoprotein | protein | 1051 | 19% helix, 28% strand | P0DTC2 |
| c | Heavy chain of S3H3 Fab | protein | 118 | 0% helix, 52% strand | — |
| d | Light chain of S3H3 Fab | protein | 111 | 3% helix, 44% strand | — |
| a | Heavy chain of S3H3 Fab | protein | 217 | 5% helix, 52% strand | — |
| b | Light chain of S3H3 Fab | protein | 215 | 7% 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 | 726 | 0.86 | 0.90 | 117 | empty |
| 2 | 918 | 0.85 | 0.87 | 108 | empty |
| 3 | 812 | 0.85 | 0.87 | 109 | empty |
| 4 | 504 | 0.83 | 0.89 | 60 | empty |
| 5 | 499 | 0.81 | 0.88 | 51 | empty |
Interfaces
9 interfaces between chains.
- A–B · 5642 Ų buried · 34 hydrogen bonds · protein-protein
- C–B · 5490 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 4450 Ų buried · 36 hydrogen bonds · protein-protein
- a–b · 1814 Ų buried · 19 hydrogen bonds · protein-protein
- c–d · 926 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide (disulfide).
Compared structures
- 7WK9 · SARS-CoV-2 Omicron open 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 7WK9 · PDBe 7WK9 · UniProt P0DTC2
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