Research workbench
Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the GP41 fp-mper HYB3K construct 514GIGALFLGFLGAAGS528KK-ahx-655KNEQELLELDKWASLWN671 soaked in PEG/2- propanol solution
Analyse Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DRQ
- Type
- protein
- Length
- 437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2F5 Fab' light chain; 2F5 Fab' heavy chain; GP41 peptide epitope
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2F5 Fab' light chain | protein | 213 | 6% helix, 52% strand | — |
| B | 2F5 Fab' heavy chain | protein | 216 | 6% helix, 50% strand | — |
| C | GP41 peptide epitope | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 446 | 0.59 | 0.75 | 57 | empty |
| 2 | 60 | 0.28 | 0.74 | 15 | empty |
| 3 | 57 | 0.25 | 0.72 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1811 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 339 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 298 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3DRQ · Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41… · the same entry in another collection · chain A against A, 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 3DRQ · PDBe 3DRQ
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