MolNFT v1 · #179782 · protein
Structural basis for a germline-biased antibody response to SARS-cov-2 (RBD:C1A-C2 Fab)
7KFX · Spike glycoprotein: “Structural basis for a germline-biased antibody response to SARS-cov-2 (RBD:C1A-C2 Fab)”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.59). MolNFT v1 #179782 on GenesisL1: 3D structure…
- PDB
- 7KFX
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of human antibody C1A-C2 Fab; Light chain of human…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 195 | 18% helix, 29% strand | P0DTC2 |
| H | Heavy chain of human antibody C1A-C2 Fab | protein | 225 | 7% helix, 48% strand | — |
| L | Light chain of human antibody C1A-C2 Fab | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
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 | 266 | 0.59 | 0.79 | 38 | empty |
| 2 | 141 | 0.53 | 0.81 | 26 | empty |
| 3 | 271 | 0.49 | 0.74 | 33 | empty |
| 4 | 80 | 0.39 | 0.78 | 19 | empty |
| 5 | 66 | 0.28 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1924 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 916 Ų buried · 23 hydrogen bonds · protein-protein
- A–L · 419 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7KFX · Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 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 7KFX · PDBe 7KFX · UniProt P0DTC2
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