Research workbench
TCR mimic antibody (Fab fragment)
Analyse TCR mimic antibody (Fab fragment) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RE9
- Type
- protein
- Length
- 840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 209 | 4% helix, 55% strand | — |
| L | Fab light chain | protein | 210 | 6% helix, 51% strand | — |
| A | Fab heavy chain | protein | 210 | 7% helix, 55% strand | — |
| B | Fab light chain | protein | 211 | 6% helix, 51% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains H, A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.68 | 0.74 | 70 | PEG |
| 2 | 90 | 0.59 | 0.87 | 24 | empty |
| 3 | 279 | 0.50 | 0.73 | 28 | empty |
| 4 | 246 | 0.48 | 0.74 | 38 | PEG |
| 5 | 52 | 0.33 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1639 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1584 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 994 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7RE9 · TCR mimic antibody (Fab fragment) · 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 7RE9 · PDBe 7RE9
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