Research workbench
SARS-cov-2 spike in complex with the S2D106 neutralizing antibody Fab fragment (local refinement of the rbd and S2D106)
Analyse SARS-cov-2 spike in complex with the S2D106 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
- 7R7N
- Type
- protein
- Length
- 391 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2D106 Fab heavy chain; Spike glycoprotein; S2D106 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 5 · best druggability 0.71
Structure
electron microscopy · 3 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S2D106 Fab heavy chain | protein | 109 | 6% helix, 45% strand | — |
| E | Spike glycoprotein | protein | 189 | 15% helix, 29% strand | P0DTC2 |
| L | S2D106 Fab light chain | protein | 93 | 0% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.71 | 0.91 | 32 | empty |
| 2 | 85 | 0.67 | 0.92 | 24 | empty |
| 3 | 146 | 0.44 | 0.76 | 16 | empty |
| 4 | 84 | 0.34 | 0.74 | 19 | empty |
| 5 | 50 | 0.27 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 869 Ų buried · 4 hydrogen bonds · protein-protein
- H–E · 591 Ų buried · 3 hydrogen bonds · protein-protein
- E–L · 231 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7R7N · SARS-CoV-2 spike in complex with the S2D106 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 7R7N · PDBe 7R7N · UniProt P0DTC2
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