Research workbench
Structural basis for a germline-biased antibody response to SARS-cov-2 (RBD:C1A-B3 Fab)
Analyse Structural basis for a germline-biased antibody response to SARS-cov-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KFW
- Type
- protein
- Length
- 1,890 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of antibody C1A-B3 Fab; Light chain of antibody C1A-B3 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 195 | 15% helix, 29% strand | P0DTC2 |
| C, H | Heavy chain of antibody C1A-B3 Fab | protein | 222 | 7% helix, 48% strand | — |
| D, G, L | Light chain of antibody C1A-B3 Fab | protein | 214 | 6% helix, 51% strand | — |
| F | Heavy chain of antibody C1A-B3 Fab | protein | 219 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.61 | 0.74 | 46 | empty |
| 2 | 489 | 0.60 | 0.75 | 62 | empty |
| 3 | 499 | 0.59 | 0.74 | 54 | empty |
| 4 | 245 | 0.58 | 0.79 | 30 | empty |
| 5 | 55 | 0.52 | 0.88 | 21 | empty |
Interfaces
12 interfaces between chains.
- H–L · 2016 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1973 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1938 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 872 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7KFW · Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B3 Fab) · 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 7KFW · PDBe 7KFW · UniProt P0DTC2
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