Research workbench
Crystal structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a GP41 7MER epitope
Analyse Crystal structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TJG
- Type
- protein
- Length
- 458 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 2F5 light chain; Fab 2F5 heavy chain; Envelope glycoprotein GP41
- UniProt
- Q75760
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab 2F5 light chain | protein | 214 | 6% helix, 50% strand | — |
| H | Fab 2F5 heavy chain | protein | 237 | 9% helix, 50% strand | — |
| P | Envelope glycoprotein GP41 | protein | 7 | 0% helix, 14% strand | Q75760 |
Ligands and binding sites
- IPA · Isopropyl alcohol · additive · 7 copies · chains L, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.59 | 0.80 | 30 | empty |
| 2 | 290 | 0.51 | 0.74 | 37 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2032 Ų buried · 18 hydrogen bonds · protein-protein
- H–P · 373 Ų buried · 11 hydrogen bonds · protein-protein
- L–P · 247 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, alkylation).
Compared structures
- 1TJG · Crystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a… · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q75760
- Elsewhere: RCSB PDB 1TJG · PDBe 1TJG · UniProt Q75760
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