Research workbench
Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with antibody CC12.1 Fab and nanobody Nb-C4-225
Analyse Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8ELO
- Type
- protein
- Length
- 749 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.72
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2; synthetic…
- Molecule
- Spike protein S1; Nanobody Nb-C4-225; CC12.1 Fab heavy chain; CC12.1 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.72 · 4 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 192 | 12% helix, 31% strand | P0DTC2 |
| B | Nanobody Nb-C4-225 | protein | 126 | 2% helix, 52% strand | — |
| H | CC12.1 Fab heavy chain | protein | 216 | 10% helix, 51% strand | — |
| L | CC12.1 Fab light chain | protein | 215 | 6% helix, 52% 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.70 | 0.79 | 82 | empty |
| 2 | 312 | 0.52 | 0.74 | 42 | empty |
| 3 | 125 | 0.44 | 0.77 | 26 | empty |
| 4 | 154 | 0.44 | 0.75 | 25 | empty |
| 5 | 73 | 0.36 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1908 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 812 Ų buried · 18 hydrogen bonds · protein-protein
- A–L · 571 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 560 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
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 8ELO · PDBe 8ELO · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.