Research workbench
Crystal structure of potent neutralizing antibody 10-40 in complex with sarbecovirus bat RATG13 receptor-binding domain
Analyse Crystal structure of potent neutralizing antibody 10-40 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TTX
- Type
- protein
- Length
- 635 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 1040 heavy chain; 1040 light chain
- UniProt
- A0A6B9WHD3
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 195 | 11% helix, 28% strand | A0A6B9WHD3 |
| H | 1040 heavy chain | protein | 227 | 5% helix, 50% strand | — |
| L | 1040 light chain | protein | 213 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.61 | 0.74 | 56 | empty |
| 2 | 202 | 0.55 | 0.79 | 30 | empty |
| 3 | 240 | 0.52 | 0.76 | 40 | empty |
| 4 | 115 | 0.42 | 0.77 | 22 | empty |
| 5 | 55 | 0.39 | 0.81 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1823 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 779 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 352 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7TTX · Crystal structure of potent neutralizing antibody 10-40 in complex with Sarbecovirus bat… · 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 A0A6B9WHD3
- Elsewhere: RCSB PDB 7TTX · PDBe 7TTX · UniProt A0A6B9WHD3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.