Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with the monoclonal antibody M31A7
Analyse Crystal structure of SARS-cov-2 receptor binding domain in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WUE
- Type
- protein
- Length
- 1,264 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; M31A7 Fab heavy chain; M31A7 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, BMA
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike protein S1 | protein | 195 | 13% helix, 30% strand | P0DTC2 |
| C, E | M31A7 Fab heavy chain | protein | 218 | 4% helix, 45% strand | — |
| D, F | M31A7 Fab light chain | protein | 219 | 4% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, D, B, E, F
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, D, B, E, F
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.70 | 0.80 | 54 | empty |
| 2 | 694 | 0.65 | 0.75 | 58 | empty |
| 3 | 453 | 0.59 | 0.74 | 57 | empty |
| 4 | 81 | 0.57 | 0.87 | 22 | empty |
| 5 | 398 | 0.55 | 0.73 | 52 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1929 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1924 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 619 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 446 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7WUE · Crystal structure of SARS-CoV-2 Receptor Binding Domain in complex with the monoclonal… · 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 7WUE · PDBe 7WUE · UniProt P0DTC2
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