Research workbench
SARS-cov-2 S trimer with four-antibody cocktail complex
Analyse SARS-cov-2 S trimer with four-antibody cocktail complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E5S
- Type
- protein
- Length
- 5,038 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; H014 light chain; H014 heavy chain; P17 heavy chain; P17 light chain…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1072 | 22% helix, 30% strand | P0DTC2 |
| D, H | H014 light chain | protein | 105 | 0% helix, 36% strand | — |
| E, L | H014 heavy chain | protein | 120 | 0% helix, 48% strand | — |
| I, J | P17 heavy chain | protein | 120 | 5% helix, 45% strand | — |
| K, T | P17 light chain | protein | 108 | 0% helix, 49% strand | — |
| N, Q, S | FC05 light chain | protein | 109 | 5% helix, 44% strand | — |
| O | HB27 light chain | protein | 110 | 0% helix, 24% strand | — |
| P, U, V | FC05 heavy chain | protein | 120 | 3% helix, 33% strand | — |
| R | HB27 heavy chain | protein | 119 | 0% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 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 | 1050 | 0.83 | 0.84 | 112 | empty |
| 2 | 732 | 0.83 | 0.86 | 90 | empty |
| 3 | 531 | 0.80 | 0.86 | 69 | empty |
| 4 | 419 | 0.80 | 0.88 | 43 | empty |
| 5 | 600 | 0.77 | 0.83 | 61 | empty |
Interfaces
28 interfaces between chains.
- A–B · 4893 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 4319 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 4004 Ų buried · 33 hydrogen bonds · protein-protein
- Q–U · 945 Ų buried · 4 hydrogen bonds · protein-protein
- S–V · 945 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 13 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 7E5S · SARS-CoV-2 S trimer with four-antibody cocktail complex · 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 7E5S · PDBe 7E5S · UniProt P0DTC2
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