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Crystal structure of an HIV-1 neutralizing antibody 50.1 in complex with its V3 loop peptide antigen
Analyse Crystal structure of an HIV-1 neutralizing antibody 50.1 in complex with its V3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GGI
- Type
- protein
- Length
- 878 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A 50.1 Fab (light chain); IGG2A 50.1 Fab (heavy chain); HIV-1 V3 loop peptide antigen
- UniProt
- P01863
- Pockets
- 10 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | IGG2A 50.1 Fab (light chain) | protein | 215 | 4% helix, 53% strand | — |
| H, J | IGG2A 50.1 Fab (heavy chain) | protein | 215 | 4% helix, 52% strand | P01863 |
| P, Q | HIV-1 V3 loop peptide antigen | protein | 9 | 0% helix, 11% strand | — |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.55 | 0.82 | 22 | empty |
| 2 | 153 | 0.50 | 0.79 | 23 | empty |
| 3 | 82 | 0.45 | 0.80 | 17 | empty |
| 4 | 92 | 0.41 | 0.78 | 20 | empty |
| 5 | 159 | 0.40 | 0.73 | 23 | empty |
Interfaces
8 interfaces between chains.
- M–J · 1695 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1636 Ų buried · 11 hydrogen bonds · protein-protein
- H–P · 389 Ų buried · 9 hydrogen bonds · protein-protein
- J–Q · 370 Ų buried · 9 hydrogen bonds · protein-protein
- L–J · 311 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1GGI · Crystal structure of an HIV-1 neutralizing antibody 50.1 in complex with its V3 loop… · the same entry in another collection · chain Q against Q, TM-score 1.00
- P01863 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, a allele (P01863) · a predicted model of the same protein · chain J against A, TM-score 0.49
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01863
- Elsewhere: RCSB PDB 1GGI · PDBe 1GGI · UniProt P01863
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