Research workbench
Crystal structure of neutralizing antibody HJ16 in complex with HIV-1 GP120
Analyse Crystal structure of neutralizing antibody HJ16 in complex with HIV-1 GP120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YE4
- Type
- protein
- Length
- 778 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HT593.1 GP120; Heavy chain human antibody HJ16; Light chain of HJ16
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | HT593.1 GP120 | protein | 334 | 17% helix, 39% strand | — |
| H | Heavy chain human antibody HJ16 | protein | 227 | 9% helix, 53% strand | — |
| L | Light chain of HJ16 | protein | 217 | 8% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.68 | 0.83 | 45 | empty |
| 2 | 430 | 0.59 | 0.75 | 57 | empty |
| 3 | 191 | 0.58 | 0.81 | 37 | empty |
| 4 | 88 | 0.47 | 0.81 | 22 | empty |
| 5 | 131 | 0.40 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1865 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 647 Ų buried · 20 hydrogen bonds · protein-protein
- G–L · 403 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4YE4 · Crystal Structure of Neutralizing Antibody HJ16 in Complex with HIV-1 gp120 · the same entry in another collection · chain G against G, 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 4YE4 · PDBe 4YE4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.