Research workbench
Cryo-EM structure of neutralizing antibody 1-57 in complex with prefusion SARS-cov-2 spike glycoprotein
Analyse Cryo-EM structure of neutralizing antibody 1-57 in complex with prefusion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LS9
- Type
- protein
- Length
- 4,002 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 1-57 Fab heavy chain; 1-57 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1097 | 21% helix, 29% strand | P0DTC2 |
| H, D, E | 1-57 Fab heavy chain | protein | 129 | 2% helix, 50% strand | — |
| L, F, G | 1-57 Fab light chain | protein | 108 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, E, C, B, H, D
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 1156 | 0.87 | 0.88 | 147 | empty |
| 2 | 1030 | 0.83 | 0.84 | 104 | empty |
| 3 | 252 | 0.79 | 0.92 | 33 | empty |
| 4 | 1134 | 0.79 | 0.81 | 111 | empty |
| 5 | 904 | 0.79 | 0.81 | 72 | empty |
Interfaces
18 interfaces between chains.
- A–C · 7110 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 7090 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 6992 Ų buried · 64 hydrogen bonds · protein-protein
- H–L · 824 Ų buried · 5 hydrogen bonds · protein-protein
- E–G · 813 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 51 glycan (disulfide, N-glycosylation).
Compared structures
- 7LS9 · Cryo-EM structure of neutralizing antibody 1-57 in complex with prefusion SARS-CoV-2… · 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 7LS9 · PDBe 7LS9 · UniProt P0DTC2
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