Research workbench
Structure of SARS-cov-2 spike receptor-binding domain complexed with its receptor equine ACE2
Analyse Structure of SARS-cov-2 spike receptor-binding domain complexed with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W6U
- Type
- protein
- Length
- 785 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme; Spike protein S1
- EC
- 3.4.-.-
- UniProt
- F6V9L3, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme (EC 3.4.-.-) | protein | 597 | 63% helix, 4% strand | F6V9L3 |
| B | Spike protein S1 | protein | 188 | 18% helix, 26% strand | P0DTC2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.68 | 0.76 | 71 | empty |
| 2 | 481 | 0.66 | 0.78 | 44 | empty |
| 3 | 280 | 0.58 | 0.78 | 30 | empty |
| 4 | 99 | 0.37 | 0.75 | 23 | empty |
| 5 | 88 | 0.37 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 850 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7W6U · Structure of SARS-CoV-2 spike receptor-binding domain complexed with its receptor equine… · 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 F6V9L3
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7W6U · PDBe 7W6U · UniProt F6V9L3 · UniProt P0DTC2
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