MolNFT v1 · #188482 · protein
Crystal structure of potent neutralizing antibody 10-40 in complex with bat WIV1 receptor-binding domain
7TTY · Spike protein S1: “Crystal structure of potent neutralizing antibody 10-40 in complex with bat WIV1 receptor-binding domain”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.65). MolNFT v1 #188482 on GenesisL1: 3D…
- PDB
- 7TTY
- Type
- protein
- Length
- 633 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
- U5WI05
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 190 | 14% helix, 27% strand | U5WI05 |
| H | 1040 heavy chain | protein | 230 | 3% helix, 47% strand | — |
| L | 1040 light chain | protein | 213 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.65 | 0.77 | 70 | empty |
| 2 | 577 | 0.62 | 0.74 | 61 | empty |
| 3 | 224 | 0.51 | 0.76 | 41 | empty |
| 4 | 102 | 0.44 | 0.78 | 15 | empty |
| 5 | 64 | 0.31 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1876 Ų buried · 27 hydrogen bonds · protein-protein
- A–H · 780 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 304 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7TTY · Crystal structure of potent neutralizing antibody 10-40 in complex with bat WIV1… · 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 U5WI05
- Elsewhere: RCSB PDB 7TTY · PDBe 7TTY · UniProt U5WI05
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