MolNFT v1 · #172653 · protein
SARS-cov-2 spike glycoprotein with 2 ACE2 bound
7A97: “SARS-cov-2 spike glycoprotein with 2 ACE2 bound”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #172653 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7A97
- Type
- protein
- Length
- 4,373 residues
- Chains
- 5
- 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 0.87
Structure
electron microscopy · 4 distinct chains · 23% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1065 | 17% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1066 | 17% helix, 27% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1066 | 18% helix, 26% strand | P0DTC2 |
| D, E | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 588 | 55% helix, 3% 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 | 993 | 0.87 | 0.88 | 130 | empty |
| 2 | 799 | 0.85 | 0.88 | 96 | empty |
| 3 | 856 | 0.80 | 0.83 | 84 | empty |
| 4 | 490 | 0.78 | 0.85 | 34 | empty |
| 5 | 106 | 0.75 | 0.95 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4488 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 4166 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 4111 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 1051 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1023 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 7A97 · SARS-CoV-2 Spike Glycoprotein with 2 ACE2 Bound · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.98
- 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 0.98
- 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 0.97
- 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 0.97
- 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 0.97
- 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 0.97
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 7A97 · PDBe 7A97 · UniProt P0DTC2 · UniProt Q9BYF1
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