MolNFT v1 · #158770 · protein
Crystal structure of the germline PGZL1 (PGZL1_GVMDMJ) Fab in complex with mper peptide epitope.
6O42 · PGZL1_GVMDMJ light chain: “Crystal structure of the germline PGZL1 (PGZL1_GVMDMJ) Fab in complex with mper peptide epitope.”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.55). MolNFT v1 #158770 on GenesisL1: 3D…
- PDB
- 6O42
- Type
- protein
- Length
- 899 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGZL1_GVMDMJ light chain; PGZL1_GVMDMJ heavy chain; Mper peptide, region 671-683 of HIV-1…
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | PGZL1_GVMDMJ light chain | protein | 214 | 7% helix, 53% strand | — |
| H | PGZL1_GVMDMJ heavy chain | protein | 220 | 5% helix, 53% strand | — |
| B | PGZL1_GVMDMJ heavy chain | protein | 221 | 3% helix, 50% strand | — |
| G, I | Mper peptide, region 671-683 of HIV-1 GP41 | protein | 15 | 87% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.55 | 0.74 | 48 | empty |
| 2 | 355 | 0.55 | 0.74 | 49 | empty |
| 3 | 157 | 0.45 | 0.76 | 28 | empty |
| 4 | 86 | 0.35 | 0.75 | 18 | empty |
| 5 | 84 | 0.33 | 0.74 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1844 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1721 Ų buried · 14 hydrogen bonds · protein-protein
- H–G · 606 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 596 Ų buried · 8 hydrogen bonds · protein-protein
- L–A · 370 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6O42 · Crystal structure of the germline PGZL1 (PGZL1_gVmDmJ) Fab in complex with MPER peptide… · 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 6O42 · PDBe 6O42
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