Research workbench
Crystal structure of non-neutralizing, A32-like antibody 2.2C in complex with HIV-1 env GP120
Analyse Crystal structure of non-neutralizing, A32-like antibody 2.2C in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R4H
- Type
- protein
- Length
- 945 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 env GP120; T-cell surface glycoprotein CD4; Antibody 2.2C, light chain; Antibody…
- UniProt
- P01730
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 env GP120 | protein | 337 | 16% helix, 32% strand | — |
| B | T-cell surface glycoprotein CD4 | protein | 178 | 5% helix, 46% strand | P01730 |
| L | Antibody 2.2C, light chain | protein | 210 | 5% helix, 48% strand | — |
| H | Antibody 2.2C, heavy chain | protein | 220 | 8% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.69 | 0.97 | 21 | empty |
| 2 | 326 | 0.57 | 0.76 | 44 | empty |
| 3 | 308 | 0.52 | 0.74 | 43 | empty |
| 4 | 156 | 0.48 | 0.77 | 25 | empty |
| 5 | 55 | 0.48 | 0.86 | 22 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1828 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1013 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 680 Ų buried · 2 hydrogen bonds · protein-protein
- A–L · 288 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide, 8 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 4R4H · Crystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 Env… · the same entry in another collection · chain A against A, TM-score 1.00
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P01730
- Elsewhere: RCSB PDB 4R4H · PDBe 4R4H · UniProt P01730
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.