Research workbench
Crystal structure of the SARS-cov-2 rbd in complex with the ultrapotent antibody CV2.1169 and CR3022
Analyse Crystal structure of the SARS-cov-2 rbd in complex with the ultrapotent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QEZ
- Type
- protein
- Length
- 859 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; CR3022 heavy chain; CR3022 light chain; CV2.1169 IgA heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 196 | 13% helix, 30% strand | P0DTC2 |
| E | CR3022 heavy chain | protein | 214 | 7% helix, 49% strand | — |
| F | CR3022 light chain | protein | 218 | 4% helix, 51% strand | — |
| H | CV2.1169 IgA heavy chain | protein | 123 | 2% helix, 47% strand | — |
| L | CV2.1169 light chain | protein | 108 | 6% helix, 42% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.59 | 0.75 | 45 | empty |
| 2 | 69 | 0.38 | 0.78 | 14 | empty |
| 3 | 105 | 0.34 | 0.73 | 21 | empty |
| 4 | 77 | 0.34 | 0.75 | 22 | empty |
| 5 | 91 | 0.34 | 0.74 | 21 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1814 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 848 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 673 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 601 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 422 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7QEZ · Crystal structure of the SARS-CoV-2 RBD in complex with the ultrapotent antibody CV2.1169… · 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 7QEZ · PDBe 7QEZ · UniProt P0DTC2
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