Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing human antibody wrair-2057.
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
- 7N4I
- Type
- protein
- Length
- 632 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wrair-2057 antibody Fab heavy chain; Wrair-2057 antibody Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Wrair-2057 antibody Fab heavy chain | protein | 221 | 7% helix, 50% strand | — |
| L | Wrair-2057 antibody Fab light chain | protein | 212 | 7% helix, 51% strand | — |
| C | Spike protein S1 | protein | 199 | 18% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.58 | 0.77 | 32 | empty |
| 2 | 456 | 0.57 | 0.74 | 54 | empty |
| 3 | 177 | 0.56 | 0.81 | 34 | GOL |
| 4 | 71 | 0.46 | 0.83 | 24 | GOL |
| 5 | 60 | 0.32 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1707 Ų buried · 13 hydrogen bonds · protein-protein
- H–C · 681 Ų buried · 14 hydrogen bonds · protein-protein
- L–C · 292 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7N4I · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · 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 7N4I · PDBe 7N4I · UniProt P0DTC2
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