Research workbench
Structure of the SARS-cov-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022
Analyse Structure of the SARS-cov-2 receptor binding domain in complex with the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RKU
- Type
- protein
- Length
- 2,545 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; C022 antibody Fab heavy chain; C022 antibody Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 8 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike protein S1 | protein | 196 | 17% helix, 31% strand | P0DTC2 |
| C | Spike protein S1 | protein | 195 | 15% helix, 29% strand | P0DTC2 |
| D | Spike protein S1 | protein | 194 | 15% helix, 30% strand | P0DTC2 |
| E, H | C022 antibody Fab heavy chain | protein | 231 | 6% helix, 51% strand | — |
| F, L | C022 antibody Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| G | C022 antibody Fab heavy chain | protein | 223 | 5% helix, 54% strand | — |
| I, K | C022 antibody Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| J | C022 antibody Fab heavy chain | protein | 225 | 4% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.68 | 0.76 | 84 | empty |
| 2 | 441 | 0.68 | 0.80 | 50 | empty |
| 3 | 396 | 0.65 | 0.79 | 55 | empty |
| 4 | 630 | 0.63 | 0.74 | 55 | empty |
| 5 | 594 | 0.62 | 0.74 | 44 | empty |
Interfaces
22 interfaces between chains.
- H–L · 2084 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2061 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 1943 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 1894 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 777 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 5 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7RKU · Structure of the SARS-CoV-2 receptor binding domain in complex with the human… · 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 7RKU · PDBe 7RKU · UniProt P0DTC2
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