Research workbench
SARS-cov-2 spike RBDMACSP36 binding to MACE2
Analyse SARS-cov-2 spike RBDMACSP36 binding to MACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FDK
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q8R0I0, P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.71
Structure
electron microscopy · 2 distinct chains · 44% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 54% helix, 4% strand | Q8R0I0 |
| E | Spike protein S1 | protein | 194 | 11% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.71 | 0.78 | 70 | empty |
| 2 | 574 | 0.65 | 0.76 | 39 | empty |
| 3 | 62 | 0.63 | 0.92 | 19 | empty |
| 4 | 189 | 0.54 | 0.79 | 34 | empty |
| 5 | 76 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–E · 904 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 Q8R0I0
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7FDK · PDBe 7FDK · UniProt Q8R0I0 · UniProt P0DTC2
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