Research workbench
Murine T-cell receptor variable DOMAIN/FAB complex
Analyse Murine T-cell receptor variable DOMAIN/FAB complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KB5
- Type
- protein
- Length
- 665 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KB5-C20 T-cell antigen receptor; Antibody desire-1
- UniProt
- P04214, P01837, P01865
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KB5-C20 T-cell antigen receptor | protein | 115 | 3% helix, 50% strand | — |
| B | KB5-C20 T-cell antigen receptor | protein | 117 | 0% helix, 51% strand | P04214 |
| L | Antibody desire-1 | protein | 214 | 7% helix, 48% strand | P01837 |
| H | Antibody desire-1 | protein | 219 | 3% helix, 50% strand | P01865 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.79 | 0.97 | 31 | empty |
| 2 | 593 | 0.62 | 0.74 | 64 | empty |
| 3 | 78 | 0.50 | 0.84 | 19 | empty |
| 4 | 174 | 0.49 | 0.77 | 24 | empty |
| 5 | 137 | 0.42 | 0.75 | 26 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1905 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 460 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 424 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 390 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1KB5 · Murine T-cell receptor variable DOMAIN/FAB complex · the same entry in another collection · chain A against A, TM-score 1.00
- P04214 · AlphaFold monomer V2.0 prediction for T-cell receptor beta chain V region E1 (P04214) · a predicted model of the same protein · chain B against A, TM-score 0.92
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.52
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain L against A, TM-score 0.49
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P04214
- Every structure of UniProt P01837
- Every structure of UniProt P01865
- Elsewhere: RCSB PDB 1KB5 · PDBe 1KB5 · UniProt P04214 · UniProt P01837 · UniProt P01865
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