MolNFT v1 · #179101 · protein
Crystal structure of the SARS-cov-2 spike receptor-binding domain (rbd) with nanobody NB20
7JVB · Spike protein S1: “Crystal structure of the SARS-cov-2 spike receptor-binding domain (rbd) with nanobody NB20”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #179101 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7JVB
- Type
- protein
- Length
- 621 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Nanobody NB20
- UniProt
- P0DTC2
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 13% helix, 26% strand | P0DTC2 |
| C, D | Nanobody NB20 | protein | 117 | 0% helix, 50% strand | — |
| B | Spike protein S1 | protein | 193 | 13% helix, 26% strand | P0DTC2 |
Ligands and binding sites
- CAC · Cacodylate ion · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.69 | 0.92 | 19 | empty |
| 2 | 92 | 0.66 | 0.90 | 18 | empty |
| 3 | 55 | 0.60 | 0.92 | 21 | empty |
| 4 | 53 | 0.56 | 0.90 | 18 | empty |
| 5 | 113 | 0.40 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–D · 762 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 755 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7JVB · Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20 · 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 7JVB · PDBe 7JVB · UniProt P0DTC2
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