MolNFT v1 · #172650 · protein
SARS-cov-2 spike glycoprotein with 1 ACE2 bound
7A94: “SARS-cov-2 spike glycoprotein with 1 ACE2 bound”. Electron microscopy, 2 ligands (NAG, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #172650 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7A94
- Type
- protein
- Length
- 3,825 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, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1080 | 21% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1079 | 21% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1078 | 21% helix, 33% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 588 | 61% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, C, B
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1049 | 0.87 | 0.88 | 125 | empty |
| 2 | 991 | 0.87 | 0.88 | 98 | empty |
| 3 | 1187 | 0.83 | 0.84 | 121 | empty |
| 4 | 906 | 0.80 | 0.82 | 93 | empty |
| 5 | 1032 | 0.79 | 0.81 | 101 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4453 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 4377 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4119 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 867 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 23 glycan (disulfide, N-glycosylation).
Compared structures
- 7A94 · SARS-CoV-2 Spike Glycoprotein with 1 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 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 0.99
- 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 0.98
- 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 0.98
- 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 0.98
- 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 0.98
- 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 0.96
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 7A94 · PDBe 7A94 · UniProt P0DTC2 · UniProt Q9BYF1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.