Research workbench
Structure of SARS-cov-2 spike receptor-binding domain Y453F mutation complexed with american mink ACE2
Analyse Structure of SARS-cov-2 spike receptor-binding domain Y453F mutation complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W8S
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 9 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 | protein | 595 | 56% helix, 3% strand | — |
| B | Spike protein S1 | protein | 193 | 11% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.76 | 0.97 | 22 | empty |
| 2 | 1094 | 0.73 | 0.76 | 109 | empty |
| 3 | 538 | 0.68 | 0.78 | 52 | empty |
| 4 | 71 | 0.49 | 0.83 | 14 | empty |
| 5 | 82 | 0.48 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 976 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7W8S · Structure of SARS-CoV-2 spike receptor-binding domain Y453F 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 7W8S · PDBe 7W8S · UniProt P0DTC2
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