MolNFT v1 · #177043 · protein
SARS-cov-2 S trimer with three-antibody cocktail complex
7E5R · H014 light chain: “SARS-cov-2 S trimer with three-antibody cocktail complex”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #177043 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E5R
- Type
- protein
- Length
- 5,262 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H014 light chain; H014 heavy chain; Spike glycoprotein; P17 heavy chain; P17 light chain…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, D, E | H014 light chain | protein | 105 | 0% helix, 43% strand | — |
| L, N, O | H014 heavy chain | protein | 120 | 5% helix, 43% strand | — |
| A, B, C | Spike glycoprotein | protein | 1072 | 21% helix, 30% strand | P0DTC2 |
| M, T, I | P17 heavy chain | protein | 120 | 5% helix, 45% strand | — |
| U, V, K | P17 light chain | protein | 108 | 3% helix, 45% strand | — |
| R, S, Q | FC05 light chain | protein | 109 | 7% helix, 48% strand | — |
| W, X, P | FC05 heavy chain | protein | 120 | 5% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 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 | 929 | 0.85 | 0.87 | 99 | empty |
| 2 | 1038 | 0.83 | 0.84 | 106 | empty |
| 3 | 388 | 0.77 | 0.87 | 33 | empty |
| 4 | 425 | 0.75 | 0.84 | 43 | empty |
| 5 | 85 | 0.74 | 0.97 | 19 | empty |
Interfaces
30 interfaces between chains.
- A–B · 4263 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 4261 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 4195 Ų buried · 38 hydrogen bonds · protein-protein
- R–W · 787 Ų buried · 2 hydrogen bonds · protein-protein
- S–X · 764 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 7E5R · SARS-CoV-2 S trimer with three-antibody cocktail complex · the same entry in another collection · chain H against H, 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 7E5R · PDBe 7E5R · UniProt P0DTC2
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