MolNFT v1 · #158749 · protein
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).
6O3G · PGZL1 light chain: “Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1 in complex with its mper…”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.71). MolNFT v1 #158749 on…
- PDB
- 6O3G
- Type
- protein
- Length
- 1,818 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGZL1 light chain; PGZL1 heavy chain; Meper peptide, region 671-683 of HIV-1 GP41
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, D | PGZL1 light chain | protein | 214 | 5% helix, 50% strand | — |
| H | PGZL1 heavy chain | protein | 222 | 7% helix, 51% strand | — |
| A | PGZL1 heavy chain | protein | 226 | 7% helix, 53% strand | — |
| C, E | PGZL1 heavy chain | protein | 227 | 8% helix, 53% strand | — |
| F | PGZL1 light chain | protein | 210 | 7% helix, 50% strand | — |
| Q, S, G, I | Meper peptide, region 671-683 of HIV-1 GP41 | protein | 16 | 63% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.71 | 0.77 | 91 | empty |
| 2 | 618 | 0.69 | 0.78 | 80 | empty |
| 3 | 764 | 0.66 | 0.74 | 84 | empty |
| 4 | 464 | 0.59 | 0.74 | 57 | empty |
| 5 | 398 | 0.57 | 0.74 | 46 | empty |
Interfaces
18 interfaces between chains.
- F–E · 1901 Ų buried · 19 hydrogen bonds · protein-protein
- D–C · 1822 Ų buried · 14 hydrogen bonds · protein-protein
- L–H · 1822 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 1775 Ų buried · 12 hydrogen bonds · protein-protein
- C–Q · 657 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6O3G · 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 6O3G · PDBe 6O3G
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