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Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3 in complex with 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
- 6O3U
- Type
- protein
- Length
- 1,738 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGZL1.H4K3 light chain; PGZL1.H4K3 heavy chain
- Ligands
- 44E, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A, E | PGZL1.H4K3 light chain | protein | 214 | 6% helix, 51% strand | — |
| H | PGZL1.H4K3 heavy chain | protein | 221 | 9% helix, 54% strand | — |
| B | PGZL1.H4K3 heavy chain | protein | 221 | 5% helix, 53% strand | — |
| C | PGZL1.H4K3 light chain | protein | 213 | 8% helix, 52% strand | — |
| D | PGZL1.H4K3 heavy chain | protein | 219 | 3% helix, 55% strand | — |
| F | PGZL1.H4K3 heavy chain | protein | 222 | 9% helix, 55% strand | — |
Ligands and binding sites
- 44E · (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate · ligand · 8 copies · chains H, F, B, D
- SO4 · Sulfate ion · ion · 14 copies · chains H, L, A, B, D, C, F, E
- GOL · Glycerol · additive · 10 copies · chains L, H, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.76 | 0.80 | 92 | SO4 |
| 2 | 645 | 0.63 | 0.74 | 72 | SO4 |
| 3 | 451 | 0.59 | 0.75 | 68 | empty |
| 4 | 453 | 0.57 | 0.74 | 62 | GOL |
| 5 | 208 | 0.57 | 0.80 | 40 | empty |
Interfaces
14 interfaces between chains.
- E–F · 1854 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1828 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1827 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1783 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 732 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, additive adduct).
Compared structures
- 6O3U · Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3… · 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 6O3U · PDBe 6O3U
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