Research workbench
Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibodies A19-46.1 and B1-182.1
Analyse Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibodies… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TCC
- Type
- protein
- Length
- 4,750 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.86
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Heavy chain of antibody A19-46.1; Light chain of antibody A19-46.1…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.86 · 6 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1118 | 21% helix, 28% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1116 | 21% helix, 25% strand | P0DTC2 |
| D, H, M | Heavy chain of antibody A19-46.1 | protein | 126 | 5% helix, 48% strand | — |
| E, L, N | Light chain of antibody A19-46.1 | protein | 110 | 5% helix, 50% strand | — |
| J, O, F | heavy chain of antibody B1-182.1 | protein | 122 | 2% helix, 40% strand | — |
| K, P, G | Light chain of antibody B1-182.1 | protein | 108 | 0% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 41 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.87 | 0.89 | 136 | empty |
| 2 | 478 | 0.83 | 0.90 | 58 | empty |
| 3 | 1039 | 0.83 | 0.83 | 107 | empty |
| 4 | 864 | 0.80 | 0.83 | 88 | empty |
| 5 | 172 | 0.78 | 0.94 | 44 | empty |
Interfaces
27 interfaces between chains.
- A–B · 4385 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 4288 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 4157 Ų buried · 33 hydrogen bonds · protein-protein
- M–N · 976 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 933 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 7TCC · Cryo-EM structure of SARS-cov-2 omicron spike in complex with antibodies A19-46.1 and… · the same entry in another collection · chain A against A, TM-score 1.00
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 7TCC · PDBe 7TCC · UniProt P0DTC2
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