Research workbench
Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive and potent HIV-1 neutralizing antibody
Analyse Crystal structure of germline Fab PGT121, a putative precursor of the broadly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NPY
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Germline PGT121 light chain; Germline PGT121 heavy chain
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Germline PGT121 light chain | protein | 212 | 8% helix, 50% strand | — |
| H | Germline PGT121 heavy chain | protein | 232 | 8% helix, 54% strand | — |
| A | Germline PGT121 light chain | protein | 211 | 8% helix, 49% strand | — |
| B | Germline PGT121 heavy chain | protein | 229 | 9% helix, 54% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains L, H, A, B
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 | 608 | 0.73 | 0.80 | 70 | empty |
| 2 | 338 | 0.64 | 0.80 | 40 | empty |
| 3 | 320 | 0.58 | 0.77 | 55 | empty |
| 4 | 194 | 0.48 | 0.76 | 26 | empty |
| 5 | 121 | 0.45 | 0.77 | 26 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1869 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1837 Ų buried · 16 hydrogen bonds · protein-protein
- L–A · 212 Ų buried · 1 hydrogen bond · protein-protein
- H–B · 105 Ų buried · 0 hydrogen bonds · protein-protein
- L–B · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 4NPY · Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive… · 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 4NPY · PDBe 4NPY
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