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Structure of the SARS-cov-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C102
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
- 7K8M
- Type
- protein
- Length
- 612 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C102 Fab heavy chain; C102 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C102 Fab heavy chain | protein | 213 | 7% helix, 53% strand | — |
| B | C102 Fab light chain | protein | 215 | 6% helix, 53% strand | — |
| E | Spike glycoprotein | protein | 184 | 14% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.59 | 0.82 | 22 | empty |
| 2 | 234 | 0.50 | 0.75 | 42 | empty |
| 3 | 165 | 0.49 | 0.77 | 35 | empty |
| 4 | 138 | 0.40 | 0.74 | 30 | empty |
| 5 | 58 | 0.33 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1806 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 864 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 293 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7K8M · 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 7K8M · PDBe 7K8M · UniProt P0DTC2
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