Research workbench
Crystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 GP41: crystals cryoprotected with sphingomyelin (02:0 sm (D18:1/2:0)).
Analyse Crystal structure of human 4E10 Fab in complex with its peptide epitope on… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XBE
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4E10 Fab light chain; 4E10 Fab heavy chain; Peptide fragment of HIV glycoprotein (GP41)…
- Ligands
- UNL
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 4E10 Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| H | 4E10 Fab heavy chain | protein | 216 | 9% helix, 55% strand | — |
| P | Peptide fragment of HIV glycoprotein (GP41) including the region 671-683 of the mper | protein | 15 | 73% helix, 0% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.57 | 0.74 | 53 | UNL |
| 2 | 82 | 0.32 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1599 Ų buried · 11 hydrogen bonds · protein-protein
- H–P · 580 Ų buried · 5 hydrogen bonds · protein-protein
- L–P · 215 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4XBE · Crystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 gp41… · 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 4XBE · PDBe 4XBE
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