MolNFT v2 · #214750 · protein
Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state)
8JYN: “Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state)”. Electron microscopy at 3.04, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.88). MolNFT v2 #214750 on GenesisL1: 3D structure…
- PDB
- 8JYN
- Type
- protein
- Length
- 3,577 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.04
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Processed angiotensin-converting enzyme 2
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 3.04 · 4 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1010 | 20% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 985 | 21% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 986 | 22% helix, 29% strand | P0DTC2 |
| D | Processed angiotensin-converting enzyme 2 | protein | 596 | 59% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 55 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · 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 | 1124 | 0.88 | 0.89 | 114 | empty |
| 2 | 1061 | 0.87 | 0.88 | 129 | empty |
| 3 | 967 | 0.80 | 0.82 | 91 | empty |
| 4 | 1004 | 0.80 | 0.82 | 96 | empty |
| 5 | 677 | 0.77 | 0.82 | 35 | empty |
Interfaces
4 interfaces between chains.
- B–C · 4340 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 4326 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 4059 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 779 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 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 0.98
- 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 0.97
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 8JYN · PDBe 8JYN · UniProt P0DTC2 · UniProt Q9BYF1
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