MolNFT v1 · #183318 · protein
SARS-cov-2 spike rbd (dimer) in complex with two FU2 nanobodies
7NLL · Surface glycoprotein: “SARS-cov-2 spike rbd (dimer) in complex with two FU2 nanobodies”. Electron microscopy, 1 ligand (RTV), 6 pockets (best druggability 0.78). MolNFT v1 #183318 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7NLL
- Type
- protein
- Length
- 656 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface glycoprotein; Nanobody FU2
- UniProt
- A0A6H1XM27
- Ligands
- RTV
- Pockets
- 6 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Surface glycoprotein | protein | 196 | 15% helix, 26% strand | A0A6H1XM27 |
| D | Surface glycoprotein | protein | 195 | 15% helix, 26% strand | A0A6H1XM27 |
| A | Nanobody FU2 | protein | 133 | 5% helix, 45% strand | — |
| C | Nanobody FU2 | protein | 132 | 5% helix, 45% strand | — |
Ligands and binding sites
- RTV · 2-(acetylamino)-1,5-anhydro-2-deoxy-D-mannitol · ligand · 2 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.78 | 0.81 | 94 | empty |
| 2 | 106 | 0.37 | 0.74 | 24 | empty |
| 3 | 76 | 0.36 | 0.76 | 21 | empty |
| 4 | 79 | 0.36 | 0.76 | 21 | empty |
| 5 | 85 | 0.33 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–C · 772 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 766 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 550 Ų buried · 4 hydrogen bonds · protein-protein
- B–A · 548 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7NLL · SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies · the same entry in another collection · chain B against B, 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 A0A6H1XM27
- Elsewhere: RCSB PDB 7NLL · PDBe 7NLL · UniProt A0A6H1XM27
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.