MolNFT v1 · #109753 · protein
Crystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 GP41; crystals cryoprotected with rac-glycerol 1- phosphate
4XC3 · 4E10 Fab light chain: “Crystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 GP41; crystals cryoprotected…”. X-ray diffraction, 2 ligands (1GP, UNL), 4 pockets (best druggability 0.57). MolNFT v1 #109753…
- PDB
- 4XC3
- 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
- 1GP, UNL
- Pockets
- 4 · 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 | 220 | 8% helix, 55% strand | — |
| P | Modified fragment of HIV-1 glycoprotein (GP41) including the mper region 671-683 | protein | 14 | 86% helix, 0% strand | — |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · 2 copies · chains L, H
- UNL · Unknown ligand · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.57 | 0.74 | 47 | empty |
| 2 | 58 | 0.51 | 0.87 | 24 | empty |
| 3 | 95 | 0.39 | 0.77 | 22 | empty |
| 4 | 88 | 0.35 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1636 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 581 Ų buried · 3 hydrogen bonds · protein-protein
- L–P · 211 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 4XC3 · 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 4XC3 · PDBe 4XC3
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