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Structure of the SARS-cov receptor binding domain in complex with the human neutralizing antibody Fab fragment, C118
Analyse Structure of the SARS-cov 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
- 7RKS
- Type
- protein
- Length
- 1,239 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C118 antibody Fab heavy chain; C118 antibody Fab light chain; Spike protein S1
- UniProt
- P59594
- Ligands
- NAG, FUC
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | C118 antibody Fab heavy chain | protein | 220 | 8% helix, 53% strand | — |
| I | C118 antibody Fab heavy chain | protein | 222 | 8% helix, 52% strand | — |
| L, M | C118 antibody Fab light chain | protein | 214 | 7% helix, 53% strand | — |
| R | Spike protein S1 | protein | 182 | 18% helix, 30% strand | P59594 |
| S | Spike protein S1 | protein | 187 | 16% helix, 28% strand | P59594 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains R, S
- FUC · alpha-L-fucopyranose · sugar · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.77 | 0.80 | 92 | empty |
| 2 | 902 | 0.75 | 0.79 | 89 | empty |
| 3 | 350 | 0.72 | 0.84 | 51 | empty |
| 4 | 333 | 0.71 | 0.84 | 49 | empty |
| 5 | 138 | 0.61 | 0.85 | 23 | empty |
Interfaces
11 interfaces between chains.
- I–M · 1821 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1788 Ų buried · 11 hydrogen bonds · protein-protein
- I–S · 754 Ų buried · 13 hydrogen bonds · protein-protein
- H–R · 744 Ų buried · 12 hydrogen bonds · protein-protein
- H–S · 607 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7RKS · Structure of the SARS-CoV receptor binding domain in complex with the human neutralizing… · the same entry in another collection · chain I against I, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain R against E, TM-score 0.92
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain R against E, TM-score 0.92
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain R against E, TM-score 0.92
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain R against E, TM-score 0.92
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain R against E, TM-score 0.92
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain R against E, TM-score 0.92
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 P59594
- Elsewhere: RCSB PDB 7RKS · PDBe 7RKS · UniProt P59594
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