Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with antibodies CV05-163 and CR3022
Analyse Crystal structure of SARS-cov-2 receptor binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LOP
- Type
- protein
- Length
- 2,145 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CR3022 Fab heavy chain; CR3022 Fab light chain; Spike protein S1; CV05-163 Fab heavy…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W | CR3022 Fab heavy chain | protein | 215 | 6% helix, 52% strand | — |
| V | CR3022 Fab light chain | protein | 220 | 5% helix, 51% strand | — |
| B | CR3022 Fab heavy chain | protein | 218 | 6% helix, 52% strand | — |
| C | CR3022 Fab light chain | protein | 221 | 5% helix, 52% strand | — |
| Z | Spike protein S1 | protein | 194 | 16% helix, 30% strand | P0DTC2 |
| X, H | CV05-163 Fab heavy chain | protein | 227 | 6% helix, 49% strand | — |
| Y | CV05-163 Fab light chain | protein | 216 | 6% helix, 51% strand | — |
| L | CV05-163 Fab light chain | protein | 212 | 6% helix, 53% strand | — |
| A | Spike protein S1 | protein | 195 | 16% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains Z, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.81 | 0.82 | 103 | empty |
| 2 | 950 | 0.80 | 0.82 | 91 | empty |
| 3 | 896 | 0.75 | 0.78 | 69 | empty |
| 4 | 291 | 0.57 | 0.77 | 41 | empty |
| 5 | 177 | 0.56 | 0.80 | 34 | empty |
Interfaces
19 interfaces between chains.
- X–Y · 2023 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1868 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1858 Ų buried · 11 hydrogen bonds · protein-protein
- W–V · 1797 Ų buried · 16 hydrogen bonds · protein-protein
- W–Z · 672 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7LOP · Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies… · the same entry in another collection · chain W against W, 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 7LOP · PDBe 7LOP · UniProt P0DTC2
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