Research workbench
Crystal structure of SARS-cov-2 receptor binding domain complexed with nanobodies vhh E and U
Analyse Crystal structure of SARS-cov-2 receptor binding domain complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KN5
- Type
- protein
- Length
- 892 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Vhh E; Vhh U
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike protein S1 | protein | 195 | 18% helix, 29% strand | P0DTC2 |
| C, D | Vhh E | protein | 129 | 5% helix, 53% strand | — |
| E | Vhh U | protein | 121 | 5% helix, 45% strand | — |
| F | Vhh U | protein | 123 | 5% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.71 | 0.83 | 72 | empty |
| 2 | 52 | 0.69 | 0.97 | 21 | empty |
| 3 | 158 | 0.50 | 0.78 | 27 | empty |
| 4 | 91 | 0.44 | 0.79 | 20 | EDO |
| 5 | 69 | 0.42 | 0.81 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–D · 974 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 919 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 710 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 658 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 395 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KN5 · Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E… · 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 7KN5 · PDBe 7KN5 · UniProt P0DTC2
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