Research workbench
Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1 in complex with its mper peptide epitope (region 671- 683 of HIV-1 GP41) and phosphatidic acid (06:0 pa)
Analyse Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O3J
- Type
- protein
- Length
- 901 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGZL1 light chain; PGZL1 heavy chain; Mper peptide, region 671-683 of HIV-1 GP41
- Ligands
- 44E
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | PGZL1 light chain | protein | 213 | 7% helix, 50% strand | — |
| H | PGZL1 heavy chain | protein | 225 | 7% helix, 52% strand | — |
| B | PGZL1 light chain | protein | 212 | 7% helix, 50% strand | — |
| A | PGZL1 heavy chain | protein | 220 | 5% helix, 50% strand | — |
| G | Mper peptide, region 671-683 of HIV-1 GP41 | protein | 15 | 87% helix, 0% strand | — |
| I | Mper peptide, region 671-683 of HIV-1 GP41 | protein | 16 | 88% helix, 0% strand | — |
Ligands and binding sites
- 44E · (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate · ligand · 2 copies · chains H, G, A, I
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.58 | 0.75 | 51 | empty |
| 2 | 413 | 0.57 | 0.75 | 49 | empty |
| 3 | 221 | 0.50 | 0.75 | 34 | empty |
| 4 | 277 | 0.49 | 0.73 | 41 | empty |
| 5 | 80 | 0.36 | 0.77 | 17 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1774 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 1735 Ų buried · 13 hydrogen bonds · protein-protein
- H–G · 670 Ų buried · 8 hydrogen bonds · protein-protein
- A–I · 652 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 452 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6O3J · Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1 in… · 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 6O3J · PDBe 6O3J
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