MolNFT v1 · #101897 · protein
Crystal structure of broadly neutralizing antibody F045-092
4O5L · Fab F045-092 light chain: “Crystal structure of broadly neutralizing antibody F045-092”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.58). MolNFT v1 #101897 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4O5L
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab F045-092 light chain; Fab F045-092 heavy chain
- UniProt
- P0DOY3, A8K008
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab F045-092 light chain | protein | 215 | 8% helix, 51% strand | P0DOY3 |
| H | Fab F045-092 heavy chain | protein | 234 | 9% helix, 45% strand | A8K008 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.58 | 0.77 | 39 | PO4 |
| 2 | 124 | 0.50 | 0.80 | 28 | empty |
| 3 | 286 | 0.49 | 0.73 | 46 | empty |
| 4 | 156 | 0.48 | 0.77 | 27 | empty |
| 5 | 52 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- L–H · 1794 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4O5L · Crystal structure of broadly neutralizing antibody F045-092 · the same entry in another collection · chain L against L, TM-score 1.00
- P0DOY3 · AlphaFold monomer V2.0 prediction for immunoglobulin lambda constant 3 (P0DOY3) · a predicted model of the same protein · chain L against A, TM-score 0.48
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 P0DOY3
- Every structure of UniProt A8K008
- Elsewhere: RCSB PDB 4O5L · PDBe 4O5L · UniProt P0DOY3 · UniProt A8K008
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