Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody 47D1
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
- 7MF1
- Type
- protein
- Length
- 632 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; 47D1 Fab heavy chain; 47D1 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 17% helix, 30% strand | P0DTC2 |
| H | 47D1 Fab heavy chain | protein | 224 | 7% helix, 50% strand | — |
| L | 47D1 Fab light chain | protein | 214 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains L, A
- FUC · alpha-L-fucopyranose · sugar · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.59 | 0.74 | 48 | empty |
| 2 | 118 | 0.40 | 0.75 | 24 | empty |
| 3 | 60 | 0.38 | 0.80 | 18 | empty |
| 4 | 88 | 0.37 | 0.76 | 20 | empty |
| 5 | 75 | 0.37 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1804 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 751 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7MF1 · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · 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 7MF1 · PDBe 7MF1 · UniProt P0DTC2
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