Research workbench
Crystal structure of 10E8 Fab in complex with the mper epitope scaffold T117V2 and phosphatidylglycerol (06:0 pg)
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
- 5T85
- Type
- protein
- Length
- 598 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
- 44G
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 10E8 Fab heavy chain | protein | 232 | 10% helix, 52% strand | — |
| L | Antibody 10E8 Fab light chain | protein | 212 | 8% helix, 51% strand | — |
| G | 10E8 epitope scaffold T117V2 | protein | 154 | 41% helix, 23% strand | — |
Ligands and binding sites
- 44G · (2S)-3-{[(R)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate · ligand · chains H, L
- PGE · Triethylene glycol · additive · 2 copies · chains L, G
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 | 456 | 0.62 | 0.76 | 52 | PGE |
| 2 | 384 | 0.54 | 0.73 | 43 | empty |
| 3 | 92 | 0.42 | 0.78 | 18 | empty |
| 4 | 106 | 0.38 | 0.75 | 27 | empty |
| 5 | 83 | 0.35 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2091 Ų buried · 19 hydrogen bonds · protein-protein
- H–G · 736 Ų buried · 9 hydrogen bonds · protein-protein
- L–G · 116 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5T85 · Crystal structure of 10E8 Fab in complex with the MPER epitope scaffold T117v2 and… · the same entry in another collection · chain H against H, 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 5T85 · PDBe 5T85
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