MolNFT v1 · #187822 · protein
Cryo-EM structure of the SARS-cov-2 D614G,N501Y,E484K mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement)
7SY3 · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 D614G,N501Y,E484K mutant spike protein ectodomain bound to human ACE2…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #187822 on…
- PDB
- 7SY3
- Type
- protein
- Length
- 3,321 residues
- Chains
- 4
- 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 0.85
Structure
electron microscopy · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 841 | 24% helix, 37% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1040 | 21% helix, 35% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 844 | 23% helix, 36% strand | P0DTC2 |
| E | 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 · 62 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.85 | 0.90 | 78 | empty |
| 2 | 537 | 0.81 | 0.87 | 65 | empty |
| 3 | 1042 | 0.76 | 0.79 | 100 | empty |
| 4 | 262 | 0.76 | 0.89 | 38 | empty |
| 5 | 543 | 0.75 | 0.83 | 43 | empty |
Interfaces
4 interfaces between chains.
- B–C · 4468 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 4070 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4042 Ų buried · 37 hydrogen bonds · protein-protein
- B–E · 991 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SY3 · Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K mutant spike protein ectodomain… · 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 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
- 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
- 3SCJ · 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 0.98
- 3SCJ · 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 0.98
- 3SCK · 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 0.98
- 3SCK · 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 0.98
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 7SY3 · PDBe 7SY3 · UniProt P0DTC2 · UniProt Q9BYF1
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