Research workbench
Cryo-EM structure of SARS-cov-2 S-uk variant (B.1.1.7) in complex with angiotensin-converting enzyme 2 (ACE2) ectodomain
Analyse Cryo-EM structure of SARS-cov-2 S-uk variant (B.1.1.7) 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
- 7EDJ
- Type
- protein
- Length
- 4,836 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2 (ACE2) ectodomain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 25% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1024 | 20% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1016 | 20% helix, 25% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1008 | 20% helix, 27% strand | P0DTC2 |
| I, J, K | Angiotensin-converting enzyme 2 (ACE2) ectodomain | protein | 596 | 51% helix, 4% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 84 copies · chains A, C, B, I, J
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 | 746 | 0.85 | 0.88 | 86 | empty |
| 2 | 561 | 0.83 | 0.88 | 44 | empty |
| 3 | 471 | 0.81 | 0.88 | 68 | empty |
| 4 | 301 | 0.78 | 0.89 | 43 | empty |
| 5 | 724 | 0.77 | 0.82 | 74 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4414 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 4287 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4179 Ų buried · 29 hydrogen bonds · protein-protein
- B–J · 895 Ų buried · 7 hydrogen bonds · protein-protein
- C–K · 846 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 47 disulfide (N-glycosylation, disulfide).
Compared structures
- 7EDJ · Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7) in complex with… · 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 7EDJ · PDBe 7EDJ · UniProt P0DTC2
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