Research workbench
SARS-cov-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (local refinement of the rbd and S2K146)
Analyse SARS-cov-2 spike in complex with the S2K146 neutralizing antibody Fab fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TAS
- Type
- protein
- Length
- 417 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2K146 Fab heavy chain; S2K146 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 2 · best druggability 0.68
Structure
electron microscopy · 3 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S2K146 Fab heavy chain | protein | 120 | 3% helix, 47% strand | — |
| L | S2K146 Fab light chain | protein | 108 | 7% helix, 44% strand | — |
| E | Spike glycoprotein | protein | 189 | 13% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.68 | 0.79 | 44 | empty |
| 2 | 141 | 0.43 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 831 Ų buried · 4 hydrogen bonds · protein-protein
- H–E · 771 Ų buried · 11 hydrogen bonds · protein-protein
- L–E · 303 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7TAS · SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (local… · 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 7TAS · PDBe 7TAS · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.