MolNFT v1 · #189269 · protein
Cryo-EM structure of SARS-cov-2 S-delta variant (B.1.617.2) in complex with angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2- bound form
7V88 · 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 0.87). MolNFT v1 #189269 on…
- PDB
- 7V88
- Type
- protein
- Length
- 4,281 residues
- Chains
- 5
- 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 0.87
Structure
electron microscopy · 4 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1027 | 21% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1033 | 22% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1029 | 22% helix, 32% strand | P0DTC2 |
| F, G | Angiotensin-converting enzyme 2,ANGIOTENSIN-converting enzyme 2 (ACE2) ectodomain (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 54% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 89 copies · chains A, C, B, F, 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 | 1093 | 0.87 | 0.88 | 131 | empty |
| 2 | 432 | 0.83 | 0.91 | 66 | empty |
| 3 | 454 | 0.83 | 0.90 | 48 | empty |
| 4 | 953 | 0.78 | 0.80 | 70 | empty |
| 5 | 828 | 0.73 | 0.78 | 82 | empty |
Interfaces
5 interfaces between chains.
- B–C · 4167 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 4112 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 3805 Ų buried · 29 hydrogen bonds · protein-protein
- C–G · 833 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 799 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 glycan, 46 disulfide (N-glycosylation, disulfide).
Compared structures
- 7V88 · Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2) 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 G 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 G 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 G 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 G 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 G 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 G 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 7V88 · PDBe 7V88 · UniProt P0DTC2 · UniProt Q9BYF1
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