Research workbench
Crystal structure of 10E8 Fab in complex with the mper epitope scaffold T117V2 and phosphatidic acid (06:0 pa)
Analyse Crystal structure of 10E8 Fab in complex with the mper epitope scaffold T117V2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T80
- Type
- protein
- Length
- 594 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 10E8 Fab heavy chain; Antibody 10E8 Fab light chain; 10E8 epitope scaffold T117V2
- Ligands
- 44E
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 10E8 Fab heavy chain | protein | 232 | 5% helix, 52% strand | — |
| L | Antibody 10E8 Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| G | 10E8 epitope scaffold T117V2 | protein | 150 | 42% helix, 24% strand | — |
Ligands and binding sites
- 44E · (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate · ligand · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.62 | 0.76 | 53 | empty |
| 2 | 307 | 0.51 | 0.73 | 42 | empty |
| 3 | 121 | 0.45 | 0.78 | 23 | empty |
| 4 | 101 | 0.40 | 0.76 | 23 | empty |
| 5 | 50 | 0.32 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2204 Ų buried · 23 hydrogen bonds · protein-protein
- H–G · 706 Ų buried · 6 hydrogen bonds · protein-protein
- L–G · 72 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5T80 · PDBe 5T80
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