Research workbench
SARS CoV2 Spike ectodomain with engineered trimerized VH binder
Analyse SARS CoV2 Spike ectodomain with engineered trimerized VH binder in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JWB
- Type
- protein
- Length
- 3,289 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- autonomous human heavy chain variable domain; Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.2 · 4 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | autonomous human heavy chain variable domain | protein | 366 | 3% helix, 53% strand | — |
| A | Spike glycoprotein | protein | 991 | 22% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 986 | 23% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 946 | 23% helix, 34% strand | P0DTC2 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.86 | 0.87 | 123 | empty |
| 2 | 1187 | 0.86 | 0.86 | 117 | empty |
| 3 | 908 | 0.79 | 0.82 | 73 | empty |
| 4 | 702 | 0.71 | 0.78 | 48 | empty |
| 5 | 803 | 0.70 | 0.76 | 64 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4313 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 3953 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 3832 Ų buried · 42 hydrogen bonds · protein-protein
- D–B · 1515 Ų buried · 23 hydrogen bonds · protein-protein
- D–A · 1001 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
- 7JWB · SARS COV2 spike ectodomain with engineered trimerized vh binder · 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 7JWB · PDBe 7JWB · UniProt P0DTC2
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