Research workbench
Crystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 GP41; crystals cryoprotected with phosphatidylcholine (03:0 pc)
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
- 4XCF
- Type
- protein
- Length
- 448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4E10 Fab light chain; 4E10 Fab heavy chain; Modified fragment of HIV-1 glycoprotein…
- Ligands
- 43Y
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 9% 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 | 218 | 7% helix, 54% strand | — |
| P | Modified fragment of HIV-1 glycoprotein (GP41) including the mper region 671-683 | protein | 16 | 81% helix, 0% strand | — |
Ligands and binding sites
- 43Y · [(2R)-3-[oxidanyl-[2-(trimethyl-$L^{4}-azanyl) ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate · ligand · 4 copies · chains L, H
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 | 359 | 0.54 | 0.74 | 53 | empty |
| 2 | 77 | 0.40 | 0.78 | 16 | empty |
| 3 | 87 | 0.32 | 0.73 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1635 Ų buried · 9 hydrogen bonds · protein-protein
- H–P · 551 Ų buried · 3 hydrogen bonds · protein-protein
- L–P · 218 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4XCF · 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 4XCF · PDBe 4XCF
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