Research workbench
Cryo-EM structure of SARS-cov-2 omicron spike in complex with antibody A19-46.1
Analyse Cryo-EM structure of SARS-cov-2 omicron spike in complex with antibody A19-46.1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TCA
- Type
- protein
- Length
- 4,244 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 0.89
Structure
electron microscopy · 4 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1114 | 19% helix, 24% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 1118 | 21% helix, 25% strand | P0DTC2 |
| D, H | Heavy chain of antibody A19-46.1 | protein | 231 | 8% helix, 49% strand | — |
| E, L | Light chain of antibody A19-46.1 | protein | 216 | 9% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 56 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 | 959 | 0.89 | 0.90 | 104 | empty |
| 2 | 1049 | 0.86 | 0.87 | 120 | empty |
| 3 | 683 | 0.82 | 0.86 | 73 | empty |
| 4 | 613 | 0.80 | 0.85 | 88 | empty |
| 5 | 183 | 0.79 | 0.93 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–B · 5147 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 4619 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 4411 Ų buried · 26 hydrogen bonds · protein-protein
- H–L · 1831 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1710 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 40 glycan (disulfide, N-glycosylation).
Compared structures
- 7TCA · Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibody A19-46.1 · 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 7TCA · PDBe 7TCA · UniProt P0DTC2
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