Research workbench
Crystal structure of the principal neutralizing site of HIV- 1
Analyse Crystal structure of the principal neutralizing site of HIV- 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ACY
- Type
- protein
- Length
- 446 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa 59.1 Fab (light chain); IGG1-kappa 59.1 Fab (heavy chain); HIV-1 GP120 (mn…
- UniProt
- P01869, P05877
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa 59.1 Fab (light chain) | protein | 215 | 6% helix, 55% strand | — |
| H | IGG1-kappa 59.1 Fab (heavy chain) | protein | 221 | 5% helix, 52% strand | P01869 |
| P | HIV-1 GP120 (mn isolate) | protein | 10 | 30% helix, 0% strand | P05877 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.57 | 0.74 | 46 | empty |
| 2 | 103 | 0.38 | 0.75 | 17 | empty |
| 3 | 53 | 0.27 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1781 Ų buried · 16 hydrogen bonds · protein-protein
- H–P · 332 Ų buried · 2 hydrogen bonds · protein-protein
- L–P · 269 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1ACY · Crystal structure of the principal neutralizing site of HIV-1 · the same entry in another collection · chain L against L, TM-score 1.00
- P01869 · AlphaFold monomer V2.0 prediction for ig gamma-1 chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.51
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 P01869
- Every structure of UniProt P05877
- Elsewhere: RCSB PDB 1ACY · PDBe 1ACY · UniProt P01869 · UniProt P05877
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.