Research workbench
Crystal structure of potent neutralizing antibody 10-40 in complex with sarbecovirus bat SHC014 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
- 7TTM
- Type
- protein
- Length
- 636 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; 1040 heavy chain; 1040 light chain
- UniProt
- U5WLK5
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 15% helix, 30% strand | U5WLK5 |
| H | 1040 heavy chain | protein | 228 | 7% helix, 50% strand | — |
| L | 1040 light chain | protein | 213 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.56 | 0.78 | 31 | empty |
| 2 | 302 | 0.50 | 0.73 | 44 | empty |
| 3 | 198 | 0.49 | 0.76 | 26 | empty |
| 4 | 129 | 0.43 | 0.77 | 31 | empty |
| 5 | 73 | 0.38 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1742 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 737 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 296 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7TTM · 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 U5WLK5
- Elsewhere: RCSB PDB 7TTM · PDBe 7TTM · UniProt U5WLK5
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