MolNFT v1 · #184317 · protein
Crystal structure of the SARS-cov-2 rbd with neutralizing-vhhs RE5D06 and RE9F06
7OLZ · Nanobody RE5D06: “Crystal structure of the SARS-cov-2 rbd with neutralizing-vhhs RE5D06 and RE9F06”. X-ray diffraction, 2 ligands (DMX, SO4), 5 pockets (best druggability 0.47). MolNFT v1 #184317 on GenesisL1: 3D structure, binding…
- PDB
- 7OLZ
- Type
- protein
- Length
- 422 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody RE5D06; Nanobody RE9F06; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- DMX, SO4
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Nanobody RE5D06 | protein | 129 | 5% helix, 52% strand | — |
| B | Nanobody RE9F06 | protein | 122 | 10% helix, 47% strand | — |
| A | Spike protein S1 | protein | 171 | 19% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- DMX · 3-[benzyl(dimethyl)ammonio]propane-1-sulfonate · ligand · chains C
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.47 | 0.84 | 16 | DMX |
| 2 | 127 | 0.45 | 0.76 | 20 | empty |
| 3 | 100 | 0.37 | 0.75 | 26 | empty |
| 4 | 51 | 0.29 | 0.76 | 12 | empty |
| 5 | 82 | 0.29 | 0.72 | 15 | empty |
Interfaces
2 interfaces between chains.
- C–A · 1054 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 689 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7OLZ · Crystal structure of the SARS-CoV-2 RBD with neutralizing-VHHs Re5D06 and Re9F06 · the same entry in another collection · chain C against C, 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 7OLZ · PDBe 7OLZ · UniProt P0DTC2
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