Research workbench
Structure of SARS-CoV-2 spike receptor-binding domain F486L mutation complexed with American mink ACE2
Analyse Structure of SARS-CoV-2 spike receptor-binding domain F486L mutation complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WA1
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.71
Structure
electron microscopy · resolution 2.9 · 2 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 | protein | 595 | 60% helix, 4% strand | — |
| B | Spike protein S1 | protein | 195 | 11% helix, 26% strand | P0DTC2 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.97 | 16 | empty |
| 2 | 635 | 0.68 | 0.77 | 70 | empty |
| 3 | 371 | 0.65 | 0.79 | 39 | empty |
| 4 | 312 | 0.58 | 0.77 | 28 | empty |
| 5 | 59 | 0.36 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7WA1 · Structure of SARS-cov-2 spike receptor-binding domain F486L mutation complexed 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 7WA1 · PDBe 7WA1 · UniProt P0DTC2
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