MolNFT v1 · #189271 · protein
Cryo-EM structure of SARS-cov-2 S-delta variant (B.1.617.2) in complex with angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2- bound form conformation 2
7V8A · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 S-delta variant (B.1.617.2) in complex with angiotensin-converting enzyme 2…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #189271 on…
- PDB
- 7V8A
- Type
- protein
- Length
- 4,869 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2,ANGIOTENSIN-converting enzyme 2…
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1027 | 21% helix, 31% strand | P0DTC2 |
| F, G, H | Angiotensin-converting enzyme 2,ANGIOTENSIN-converting enzyme 2 (ACE2) ectodomain (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 55% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 92 copies · chains A, C, B, F, H, G
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 | 1026 | 0.88 | 0.89 | 129 | empty |
| 2 | 738 | 0.87 | 0.91 | 78 | empty |
| 3 | 199 | 0.74 | 0.90 | 38 | empty |
| 4 | 664 | 0.74 | 0.80 | 46 | empty |
| 5 | 678 | 0.69 | 0.77 | 61 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4001 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 3813 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 3755 Ų buried · 37 hydrogen bonds · protein-protein
- C–H · 897 Ų buried · 12 hydrogen bonds · protein-protein
- B–G · 873 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7V8A · Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2) in complex with… · the same entry in another collection · chain B against B, 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 7V8A · PDBe 7V8A · UniProt P0DTC2 · UniProt Q9BYF1
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