Research workbench
Rational development of high-affinity T-cell receptor-like antibodies
Analyse Rational development of high-affinity T-cell receptor-like antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GJE
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| H, B | Fab heavy chain | protein | 220 | 10% helix, 51% strand | — |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.71 | 0.75 | 102 | empty |
| 2 | 831 | 0.70 | 0.76 | 90 | empty |
| 3 | 787 | 0.70 | 0.76 | 69 | empty |
| 4 | 805 | 0.68 | 0.75 | 78 | empty |
| 5 | 84 | 0.47 | 0.82 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1743 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1702 Ų buried · 12 hydrogen bonds · protein-protein
- H–B · 1037 Ų buried · 7 hydrogen bonds · protein-protein
- L–A · 250 Ų buried · 1 hydrogen bond · protein-protein
- H–A · 115 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3GJE · Rational development of high-affinity T-cell receptor-like antibodies · 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 3GJE · PDBe 3GJE
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