MolNFT v1 · #96923 · protein
Crystal structure of human Fab PGT123, a broadly reactive and potent HIV-1 neutralizing antibody
4JY6 · PGT123 light chain: “Crystal structure of human Fab PGT123, a broadly reactive and potent HIV-1 neutralizing antibody”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.59). MolNFT v1 #96923 on GenesisL1: 3D…
- PDB
- 4JY6
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGT123 light chain; PGT123 heavy chain
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PGT123 light chain | protein | 208 | 6% helix, 49% strand | — |
| B | PGT123 heavy chain | protein | 230 | 8% helix, 53% strand | — |
| C | PGT123 light chain | protein | 206 | 6% helix, 49% strand | — |
| D | PGT123 heavy chain | protein | 231 | 9% helix, 52% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.59 | 0.76 | 40 | empty |
| 2 | 389 | 0.58 | 0.75 | 45 | empty |
| 3 | 322 | 0.54 | 0.75 | 34 | empty |
| 4 | 50 | 0.48 | 0.86 | 15 | empty |
| 5 | 63 | 0.40 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2027 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2005 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 239 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4JY6 · Crystal structure of human Fab PGT123, a broadly reactive and potent HIV-1 neutralizing… · 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
- Elsewhere: RCSB PDB 4JY6 · PDBe 4JY6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.