Research workbench
Crystal structure of SARS-cov-2 receptor binding domain complexed with nanobody vhh W and antibody Fab CC12.3
Analyse Crystal structure of SARS-cov-2 receptor binding domain complexed with nanobody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KN7
- Type
- protein
- Length
- 744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Vhh W; CC12.3 Fab heavy chain; CC12.3 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 189 | 16% helix, 29% strand | P0DTC2 |
| B | Vhh W | protein | 125 | 7% helix, 47% strand | — |
| H | CC12.3 Fab heavy chain | protein | 217 | 7% helix, 53% strand | — |
| L | CC12.3 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.76 | 0.78 | 127 | empty |
| 2 | 413 | 0.58 | 0.75 | 58 | empty |
| 3 | 172 | 0.45 | 0.75 | 32 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1716 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 726 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 689 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 225 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 119 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7KN7 · Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and… · the same entry in another collection · chain L against L, 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 7KN7 · PDBe 7KN7 · UniProt P0DTC2
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