Research workbench
Furin cleaved alpha variant SARS-cov-2 spike in complex with 3 ACE2
Analyse Furin cleaved alpha variant SARS-cov-2 spike in complex with 3 ACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R1A
- Type
- protein
- Length
- 4,758 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 998 | 22% helix, 29% strand | P0DTC2 |
| D, E, F | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 588 | 58% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 3 copies · chains D, E, F
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 | 668 | 0.82 | 0.86 | 58 | empty |
| 2 | 396 | 0.78 | 0.87 | 55 | empty |
| 3 | 322 | 0.77 | 0.88 | 48 | empty |
| 4 | 541 | 0.76 | 0.84 | 64 | empty |
| 5 | 257 | 0.76 | 0.89 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4068 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 4064 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 4061 Ų buried · 27 hydrogen bonds · protein-protein
- F–C · 908 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 905 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7R1A · Furin Cleaved Alpha Variant SARS-CoV-2 Spike in complex with 3 ACE2 · the same entry in another collection · chain C against C, 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 D against A, TM-score 0.99
- 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 0.99
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 7R1A · PDBe 7R1A · UniProt P0DTC2 · UniProt Q9BYF1
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