MolNFT v2 · #224881 · protein
Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with antibody O5C2
8XBF · Spike glycoprotein: “Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with antibody O5C2”. Electron microscopy at 3.6, 1 ligand (NAG), 20 pockets (best druggability 0.89). MolNFT v2 #224881 on GenesisL1: 3D structure, binding sites…
- PDB
- 8XBF
- Type
- protein
- Length
- 3,833 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; O5C2, heavy chain; O5C2, light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 3.6 · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1129 | 21% helix, 26% strand | P0DTC2 |
| D, F | O5C2, heavy chain | protein | 114 | 5% helix, 52% strand | — |
| E, G | O5C2, light chain | protein | 109 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.89 | 0.90 | 122 | empty |
| 2 | 962 | 0.83 | 0.85 | 113 | empty |
| 3 | 856 | 0.83 | 0.85 | 95 | empty |
| 4 | 933 | 0.83 | 0.85 | 113 | empty |
| 5 | 1085 | 0.83 | 0.84 | 118 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4709 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 4658 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 4620 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 682 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide, 18 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 8XBF · PDBe 8XBF · UniProt P0DTC2
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