Research workbench
Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a thioether-linked peptide encompassing the 4E10 epitope on GP41
Analyse Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FX9
- Type
- protein
- Length
- 910 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 4E10; Fragment of HIV glycoprotein GP41
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Fab 4E10 | protein | 214 | 7% helix, 49% strand | — |
| H, I | Fab 4E10 | protein | 227 | 9% helix, 53% strand | — |
| P, Q | Fragment of HIV glycoprotein GP41 | protein | 14 | 86% helix, 0% strand | — |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.56 | 0.75 | 41 | empty |
| 2 | 60 | 0.55 | 0.89 | 21 | empty |
| 3 | 325 | 0.53 | 0.74 | 38 | empty |
| 4 | 272 | 0.51 | 0.74 | 35 | empty |
| 5 | 201 | 0.48 | 0.75 | 33 | empty |
Interfaces
6 interfaces between chains.
- M–I · 1728 Ų buried · 9 hydrogen bonds · protein-protein
- L–H · 1644 Ų buried · 9 hydrogen bonds · protein-protein
- I–Q · 579 Ų buried · 4 hydrogen bonds · protein-protein
- H–P · 532 Ų buried · 4 hydrogen bonds · protein-protein
- L–P · 226 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 2FX9 · Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked… · 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
- Elsewhere: RCSB PDB 2FX9 · PDBe 2FX9
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