MolNFT v1 · #99523 · protein
Crystal structure of broadly neutralizing Fab 5J8
4M5Y · Fab 5J8 heavy chain: “Crystal structure of broadly neutralizing Fab 5J8”. X-ray diffraction, 8 pockets (best druggability 0.56). MolNFT v1 #99523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4M5Y
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 5J8 heavy chain; Fab 5J8 light chain
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab 5J8 heavy chain | protein | 217 | 11% helix, 52% strand | — |
| L, M | Fab 5J8 light chain | protein | 211 | 8% helix, 50% strand | — |
| I | Fab 5J8 heavy chain | protein | 224 | 11% helix, 51% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains H, L, I, M
- PG4 · Tetraethylene glycol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.56 | 0.74 | 50 | PEG |
| 2 | 297 | 0.53 | 0.75 | 46 | empty |
| 3 | 292 | 0.51 | 0.74 | 31 | PEG |
| 4 | 325 | 0.50 | 0.73 | 41 | empty |
| 5 | 50 | 0.40 | 0.82 | 15 | empty |
Interfaces
3 interfaces between chains.
- I–M · 1810 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1753 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 476 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4M5Y · Crystal structure of broadly neutralizing Fab 5J8 · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 4M5Y · PDBe 4M5Y
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