Research workbench
Cryo-EM structure of SARS-cov-2 2P S ectodomain bound domain-swapped antibody 2G12 from masked 3D refinement
Analyse Cryo-EM structure of SARS-cov-2 2P S ectodomain bound domain-swapped antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L09
- Type
- protein
- Length
- 3,776 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 2G12 heavy chain; 2G12 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 972 | 23% helix, 33% strand | P0DTC2 |
| H, M | 2G12 heavy chain | protein | 218 | 7% helix, 53% strand | — |
| K | 2G12 light chain | protein | 213 | 6% helix, 54% strand | — |
| L | 2G12 light chain | protein | 211 | 6% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 58 copies · chains A, M, B, C
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains M, K, A, H, L
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains H, M, K, L
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 | 748 | 0.85 | 0.88 | 97 | empty |
| 2 | 560 | 0.84 | 0.89 | 76 | empty |
| 3 | 333 | 0.79 | 0.89 | 42 | empty |
| 4 | 399 | 0.78 | 0.87 | 53 | empty |
| 5 | 481 | 0.77 | 0.85 | 72 | empty |
Interfaces
10 interfaces between chains.
- A–B · 5114 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 5032 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 5009 Ų buried · 45 hydrogen bonds · protein-protein
- H–K · 1032 Ų buried · 7 hydrogen bonds · protein-protein
- H–L · 1017 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 44 glycan (disulfide, N-glycosylation).
Compared structures
- 7L09 · Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound domain-swapped antibody 2G12 from… · 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 7L09 · PDBe 7L09 · UniProt P0DTC2
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