Research workbench
Cryo-EM structure of SARS-cov-2 S-gamma variant (P.1) in complex with angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2-bound form
Analyse Cryo-EM structure of SARS-cov-2 S-gamma variant (P.1) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V81
- Type
- protein
- Length
- 4,311 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2,GREEN fluorescent protein
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1038 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1043 | 22% helix, 30% strand | P0DTC2 |
| D, E | Angiotensin-converting enzyme 2,GREEN fluorescent protein (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 52% helix, 2% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 81 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1053 | 0.88 | 0.89 | 105 | empty |
| 2 | 1101 | 0.87 | 0.88 | 129 | empty |
| 3 | 1066 | 0.78 | 0.80 | 82 | empty |
| 4 | 868 | 0.74 | 0.78 | 77 | empty |
| 5 | 739 | 0.73 | 0.79 | 83 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4194 Ų buried · 39 hydrogen bonds · protein-protein
- C–B · 3901 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 3781 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 946 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 838 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 glycan, 44 disulfide (N-glycosylation, disulfide).
Compared structures
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D 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 D 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 D 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 D 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 D 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 D 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 7V81 · PDBe 7V81 · UniProt P0DTC2 · UniProt Q9BYF1
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