Research workbench
Crystal structure of 10E8 Fab in complex with the mper epitope scaffold T117V2
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
- 5T6L
- Type
- protein
- Length
- 1,176 residues
- Chains
- 6
- 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
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 10E8 Fab heavy chain | protein | 224 | 7% helix, 50% strand | — |
| L, B | Antibody 10E8 Fab light chain | protein | 212 | 8% helix, 50% strand | — |
| A | Antibody 10E8 Fab heavy chain | protein | 223 | 9% helix, 50% strand | — |
| G | 10E8 epitope scaffold T117V2 | protein | 153 | 42% helix, 24% strand | — |
| I | 10E8 epitope scaffold T117V2 | protein | 152 | 43% helix, 24% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 17 copies · chains H, I, L, A, G, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.69 | 0.75 | 80 | EPE |
| 2 | 578 | 0.68 | 0.78 | 49 | GOL |
| 3 | 619 | 0.68 | 0.77 | 50 | GOL |
| 4 | 346 | 0.54 | 0.74 | 46 | GOL |
| 5 | 282 | 0.52 | 0.75 | 50 | GOL |
Interfaces
7 interfaces between chains.
- H–L · 2086 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2040 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 754 Ų buried · 7 hydrogen bonds · protein-protein
- H–I · 754 Ų buried · 2 hydrogen bonds · protein-protein
- H–A · 478 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 5T6L · PDBe 5T6L
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