Research workbench
SARS-cov-2 spike glycoprotein with 3 ACE2 bound
Analyse SARS-cov-2 spike glycoprotein with 3 ACE2 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A98
- Type
- protein
- Length
- 4,962 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1066 | 17% helix, 26% strand | P0DTC2 |
| D, E, F | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 588 | 55% helix, 2% 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 | 869 | 0.86 | 0.88 | 119 | empty |
| 2 | 382 | 0.83 | 0.91 | 29 | empty |
| 3 | 426 | 0.79 | 0.88 | 46 | empty |
| 4 | 422 | 0.79 | 0.88 | 48 | empty |
| 5 | 1039 | 0.79 | 0.81 | 99 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3990 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 3990 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 3967 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 947 Ų buried · 11 hydrogen bonds · protein-protein
- E–B · 939 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide (disulfide).
Compared structures
- 7A98 · SARS-CoV-2 Spike Glycoprotein with 3 ACE2 Bound · the same entry in another collection · chain B against B, TM-score 1.00
- 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 0.97
- 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 0.97
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 P0DTC2
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7A98 · PDBe 7A98 · UniProt P0DTC2 · UniProt Q9BYF1
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