MolNFT v1 · #158753 · protein
Crystal structure of the unbound Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3
6O3K · PGZL1.H4K3 light chain: “Crystal structure of the unbound Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.58). MolNFT v1 #158753 on GenesisL1: 3D…
- PDB
- 6O3K
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGZL1.H4K3 light chain; PGZL1.H4K3 heavy chain
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | PGZL1.H4K3 light chain | protein | 214 | 7% helix, 50% strand | — |
| H | PGZL1.H4K3 heavy chain | protein | 218 | 8% helix, 54% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.58 | 0.75 | 49 | empty |
| 2 | 52 | 0.49 | 0.87 | 23 | GOL |
| 3 | 116 | 0.47 | 0.79 | 18 | empty |
| 4 | 90 | 0.43 | 0.79 | 16 | empty |
| 5 | 59 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 1765 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6O3K · Crystal structure of the unbound Fab fragment of the human HIV-1 neutralizing antibody… · the same entry in another collection · chain L against L, 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 6O3K · PDBe 6O3K
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.