MolNFT v1 · #168056 · protein
Crystal structure of SARS-cov-2 receptor binding domain in complex with human antibody CR3022
6W41 · CR3022 Fab heavy chain: “Crystal structure of SARS-cov-2 receptor binding domain in complex with human antibody CR3022”. X-ray diffraction, 2 ligands (NAG, SO4), 10 pockets (best druggability 0.52). MolNFT v1 #168056 on GenesisL1…
- PDB
- 6W41
- Type
- protein
- Length
- 638 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CR3022 Fab heavy chain; CR3022 Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CR3022 Fab heavy chain | protein | 222 | 5% helix, 50% strand | — |
| L | CR3022 Fab light chain | protein | 221 | 6% helix, 50% strand | — |
| C | Spike protein S1 | protein | 195 | 12% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains L
- GOL · Glycerol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.52 | 0.79 | 28 | empty |
| 2 | 251 | 0.47 | 0.73 | 36 | empty |
| 3 | 84 | 0.42 | 0.79 | 19 | empty |
| 4 | 108 | 0.41 | 0.77 | 23 | empty |
| 5 | 68 | 0.35 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1945 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 624 Ų buried · 10 hydrogen bonds · protein-protein
- L–C · 445 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6W41 · Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody… · the same entry in another collection · chain H against H, 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 6W41 · PDBe 6W41 · UniProt P0DTC2
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