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Cryo-EM structure of SARS-cov-2 spike in complex with antibodies B1- 182.1 and A19-61.1
Analyse Cryo-EM structure of SARS-cov-2 spike in complex with antibodies B1- 182.1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TB8
- Type
- protein
- Length
- 4,189 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; The heavy chain of SARS-cov-2 antibody A19-61.1; The light chain of…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 7 distinct chains · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1085 | 19% helix, 28% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1088 | 19% helix, 27% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1088 | 19% helix, 28% strand | P0DTC2 |
| D, F, J | The heavy chain of SARS-cov-2 antibody A19-61.1 | protein | 126 | 0% helix, 49% strand | — |
| E, G, K | The light chain of SARS-cov-2 antibody A19-61.1 | protein | 107 | 0% helix, 43% strand | — |
| H | The heavy chain of SARS-cov-2 antiboddy antibody B1-182.1 | protein | 122 | 0% helix, 30% strand | — |
| L | The light chain of SARS-cov-2 antibody B1-182.1 | protein | 107 | 0% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 43 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 | 969 | 0.87 | 0.88 | 132 | empty |
| 2 | 985 | 0.86 | 0.88 | 86 | empty |
| 3 | 1047 | 0.82 | 0.83 | 99 | empty |
| 4 | 792 | 0.81 | 0.84 | 85 | empty |
| 5 | 577 | 0.78 | 0.84 | 52 | empty |
Interfaces
17 interfaces between chains.
- B–C · 4699 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 4380 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 4100 Ų buried · 31 hydrogen bonds · protein-protein
- H–L · 881 Ų buried · 0 hydrogen bonds · protein-protein
- J–K · 810 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 33 glycan (disulfide, N-glycosylation).
Compared structures
- 7TB8 · Cryo-EM structure of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 · 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 7TB8 · PDBe 7TB8 · UniProt P0DTC2
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