MolNFT v1 · #96921 · protein
Crystal structure of human Fab PGT121, a broadly reactive and potent HIV-1 neutralizing antibody
4JY4 · PGT121 heavy chain: “Crystal structure of human Fab PGT121, a broadly reactive and potent HIV-1 neutralizing antibody”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.45). MolNFT v1 #96921 on GenesisL1…
- PDB
- 4JY4
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGT121 heavy chain; PGT121 light chain
- Ligands
- NAG, MAN, BMA, GAL, SIA, FUC
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | PGT121 heavy chain | protein | 232 | 10% helix, 54% strand | — |
| A | PGT121 light chain | protein | 208 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- GAL · beta-D-galactopyranose · sugar
- SIA · N-acetyl-alpha-neuraminic acid · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- GOL · Glycerol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.45 | 0.73 | 36 | GOL |
| 2 | 89 | 0.36 | 0.75 | 23 | empty |
| 3 | 63 | 0.34 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 2072 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4JY4 · Crystal structure of human Fab PGT121, a broadly reactive and potent HIV-1 neutralizing… · the same entry in another collection · chain B against B, 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 4JY4 · PDBe 4JY4
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