MolNFT v2 · #226081 · protein
SARS-CoV-2 Spike (BA.1) in complex with Fab of JH-8B
8YZ6 · Spike glycoprotein: “SARS-CoV-2 Spike (BA.1) in complex with Fab of JH-8B”. Electron microscopy at 4.55, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.83). MolNFT v2 #226081 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8YZ6
- Type
- protein
- Length
- 3,161 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.55
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Fab heavy chain of JH-8B; Fab light chain of JH-8B
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 4.55 · 5 distinct chains · 21% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 959 | 23% helix, 22% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 984 | 22% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 990 | 23% helix, 23% strand | P0DTC2 |
| D | Fab heavy chain of JH-8B | protein | 118 | 5% helix, 50% strand | — |
| E | Fab light chain of JH-8B | protein | 110 | 3% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar
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 | 476 | 0.83 | 0.90 | 73 | empty |
| 2 | 809 | 0.83 | 0.85 | 67 | empty |
| 3 | 316 | 0.81 | 0.91 | 41 | empty |
| 4 | 926 | 0.80 | 0.82 | 82 | empty |
| 5 | 185 | 0.80 | 0.94 | 33 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3828 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 3585 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 3539 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 789 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 465 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 12 glycan (disulfide, N-glycosylation).
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
- Elsewhere: RCSB PDB 8YZ6 · PDBe 8YZ6 · UniProt P0DTC2
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