Research workbench
Molecular basis for a potent human neutralizing antibody targeting SARS-cov-2 rbd
Analyse Molecular basis for a potent human neutralizing antibody targeting 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
- 7C01
- Type
- protein
- Length
- 1,256 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; CB6 heavy chain; CB6 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike protein S1 | protein | 195 | 15% helix, 29% strand | P0DTC2 |
| H, C | CB6 heavy chain | protein | 218 | 6% helix, 53% strand | — |
| L, D | CB6 light chain | protein | 215 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.78 | 0.83 | 85 | empty |
| 2 | 75 | 0.74 | 0.98 | 28 | empty |
| 3 | 72 | 0.71 | 0.96 | 28 | empty |
| 4 | 467 | 0.58 | 0.74 | 47 | empty |
| 5 | 403 | 0.55 | 0.74 | 43 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1925 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1866 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 775 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 774 Ų buried · 16 hydrogen bonds · protein-protein
- L–B · 523 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7C01 · Molecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD · 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 7C01 · PDBe 7C01 · UniProt P0DTC2
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