Research workbench
Fab structure of a neutralizing antibody L1 from an early subtype a HIV-1 infected patient
Analyse Fab structure of a neutralizing antibody L1 from an early subtype a HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F57
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab of a neutralizing antibody L1; Heavy chain of Fab of a neutralizing…
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of Fab of a neutralizing antibody L1 | protein | 213 | 7% helix, 50% strand | — |
| H | Heavy chain of Fab of a neutralizing antibody L1 | protein | 225 | 8% helix, 52% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.66 | 0.75 | 82 | empty |
| 2 | 93 | 0.37 | 0.76 | 23 | empty |
| 3 | 78 | 0.32 | 0.74 | 21 | empty |
| 4 | 78 | 0.32 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- L–H · 1907 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4F57 · Fab structure of a neutralizing antibody L1 from an early subtype A HIV-1 infected patient · 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 4F57 · PDBe 4F57
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