Research workbench
Crystal structure of SARS-cov-2 rbd complexed with nanosota-1
Analyse Crystal structure of SARS-cov-2 rbd complexed with nanosota-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KM5
- Type
- protein
- Length
- 620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Nanobody
- UniProt
- P0DTC2
- Ligands
- NAG, CL
- Pockets
- 10 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 8% helix, 29% strand | P0DTC2 |
| B | Spike protein S1 | protein | 195 | 10% helix, 29% strand | P0DTC2 |
| C | Nanobody | protein | 113 | 5% helix, 50% strand | — |
| D | Nanobody | protein | 118 | 5% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.47 | 0.76 | 29 | empty |
| 2 | 155 | 0.45 | 0.76 | 24 | empty |
| 3 | 76 | 0.45 | 0.81 | 20 | empty |
| 4 | 92 | 0.44 | 0.79 | 21 | empty |
| 5 | 60 | 0.40 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 917 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 891 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 653 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KM5 · Crystal structure of SARS-CoV-2 RBD complexed with Nanosota-1 · 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 7KM5 · PDBe 7KM5 · UniProt P0DTC2
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