MolNFT v1 · #142690 · protein
Trypsin-cleaved and low pH-treated SARS-cov spike glycoprotein and ACE2 complex, ACE2-free conformation with one rbd in up conformation
6ACD: “Trypsin-cleaved and low pH-treated SARS-cov spike glycoprotein and ACE2 complex, ACE2-free conformation with…”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #142690 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ACD
- Type
- protein
- Length
- 3,187 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P59594
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 18% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1065 | 18% helix, 26% strand | P59594 |
| C | Spike glycoprotein | protein | 1057 | 18% helix, 24% strand | P59594 |
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 | 427 | 0.83 | 0.91 | 60 | empty |
| 2 | 408 | 0.82 | 0.90 | 64 | empty |
| 3 | 792 | 0.82 | 0.85 | 86 | empty |
| 4 | 541 | 0.81 | 0.87 | 72 | empty |
| 5 | 768 | 0.81 | 0.84 | 92 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5561 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 5451 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 4397 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
- 6ACD · Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex… · the same entry in another collection · chain A against A, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.16
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.16
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.16
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.16
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.16
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.16
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 P59594
- Elsewhere: RCSB PDB 6ACD · PDBe 6ACD · UniProt P59594
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