Research workbench
SARS-cov-2 spike (6P) in complex with 3 R1-32 fabs and 3 ACE2, focused refinement of rbd region
Analyse SARS-cov-2 spike (6P) in complex with 3 R1-32 fabs and 3 ACE2, focused… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YDI
- Type
- protein
- Length
- 1,229 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike protein S1; Heavy chain of R1-32; Light…
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 596 | 58% helix, 4% strand | Q9BYF1 |
| E | Spike protein S1 | protein | 193 | 5% helix, 26% strand | P0DTC2 |
| H | Heavy chain of R1-32 | protein | 227 | 1% helix, 44% strand | — |
| L | Light chain of R1-32 | protein | 213 | 6% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.82 | 0.94 | 39 | empty |
| 2 | 375 | 0.72 | 0.83 | 40 | empty |
| 3 | 53 | 0.71 | 0.98 | 18 | empty |
| 4 | 325 | 0.66 | 0.81 | 40 | empty |
| 5 | 525 | 0.65 | 0.77 | 76 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1838 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 877 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 872 Ų buried · 15 hydrogen bonds · protein-protein
- E–L · 415 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7YDI · SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2, focused refinement of RBD… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7YDI · PDBe 7YDI · UniProt Q9BYF1 · UniProt P0DTC2
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