Research workbench
Cryo-EM structure of SARS-cov-2 S-kappa variant (B.1.617.1) in complex with angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2- bound form
Analyse Cryo-EM structure of SARS-cov-2 S-kappa variant (B.1.617.1) 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
- 7V85
- Type
- protein
- Length
- 4,306 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
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1038 | 20% helix, 31% strand | P0DTC2 |
| F, H | Angiotensin-converting enzyme 2,GREEN fluorescent protein (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 53% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 75 copies · chains A, C, B
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 | 1031 | 0.87 | 0.88 | 105 | empty |
| 2 | 1018 | 0.86 | 0.87 | 111 | empty |
| 3 | 193 | 0.76 | 0.91 | 42 | empty |
| 4 | 319 | 0.74 | 0.86 | 36 | empty |
| 5 | 140 | 0.74 | 0.92 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4108 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 3860 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 3460 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 955 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 903 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 44 glycan (disulfide, N-glycosylation).
Compared structures
- 7V85 · Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain H 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 H 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 H 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 H 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 7V85 · PDBe 7V85 · UniProt P0DTC2 · UniProt Q9BYF1
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