Research workbench
SARS-cov-2 spike protein in complex with ACE2, beta variant, C1 state
Analyse SARS-cov-2 spike protein in complex with ACE2, beta variant, C1 state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VXD
- Type
- protein
- Length
- 3,829 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1079 | 21% helix, 27% strand | P0DTC2 |
| D | Spike glycoprotein | protein | 1075 | 19% helix, 28% strand | P0DTC2 |
| C | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 60% helix, 4% strand | Q9BYF1 |
| B | Spike glycoprotein | protein | 1078 | 21% helix, 31% strand | P0DTC2 |
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 | 1164 | 0.85 | 0.86 | 131 | empty |
| 2 | 1144 | 0.82 | 0.83 | 97 | empty |
| 3 | 850 | 0.82 | 0.84 | 73 | empty |
| 4 | 876 | 0.80 | 0.83 | 70 | empty |
| 5 | 748 | 0.79 | 0.83 | 64 | empty |
Interfaces
4 interfaces between chains.
- D–B · 5143 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 4709 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 4368 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 1007 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide (disulfide).
Compared structures
- 7VXD · SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C1 state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
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
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7VXD · PDBe 7VXD · UniProt P0DTC2 · UniProt Q9BYF1
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