Research workbench
Cryo-EM structure of the SARS-cov-2 D614G,N501Y,E484K,K417N mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement)
Analyse Cryo-EM structure of the SARS-cov-2 D614G,N501Y,E484K,K417N mutant spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SY5
- Type
- protein
- Length
- 4,908 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Processed angiotensin-converting enzyme 2
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1040 | 21% helix, 35% strand | P0DTC2 |
| D, E, F | Processed angiotensin-converting enzyme 2 | protein | 596 | 63% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.86 | 0.87 | 143 | empty |
| 2 | 486 | 0.78 | 0.86 | 57 | empty |
| 3 | 1019 | 0.77 | 0.79 | 108 | empty |
| 4 | 395 | 0.76 | 0.86 | 59 | empty |
| 5 | 639 | 0.74 | 0.81 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4417 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 4395 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4385 Ų buried · 40 hydrogen bonds · protein-protein
- C–F · 906 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 899 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SY5 · Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417N mutant spike protein… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against A, TM-score 0.99
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
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7SY5 · PDBe 7SY5 · UniProt P0DTC2 · UniProt Q9BYF1
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