Research workbench
Trypsin-cleaved and low pH-treated SARS-cov spike glycoprotein and ACE2 complex, ACE2-bound conformation 1
Analyse Trypsin-cleaved and low pH-treated SARS-cov spike glycoprotein and ACE2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ACG
- Type
- protein
- Length
- 3,784 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23
- UniProt
- P59594, Q9BYF1
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 27% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1065 | 18% helix, 23% strand | P59594 |
| C | Spike glycoprotein | protein | 1057 | 18% helix, 21% strand | P59594 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23) | protein | 597 | 58% helix, 4% strand | Q9BYF1 |
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 | 747 | 0.88 | 0.91 | 111 | empty |
| 2 | 747 | 0.85 | 0.88 | 115 | empty |
| 3 | 932 | 0.82 | 0.83 | 101 | empty |
| 4 | 811 | 0.81 | 0.84 | 98 | empty |
| 5 | 893 | 0.80 | 0.82 | 102 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4973 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 4578 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 3963 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 969 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide (disulfide).
Compared structures
- 6ACG · Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex… · the same entry in another collection · chain B against B, 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 D against A, TM-score 0.96
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.96
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
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
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 6ACG · PDBe 6ACG · UniProt P59594 · UniProt Q9BYF1
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