Research workbench
J809.B5 TCR bound to IAB/3K
Analyse J809.B5 TCR bound to IAB/3K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P23
- Type
- protein
- Length
- 817 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- J809.B5 TCR V alpha chain (VA2.8); J809.B5 TCR V beta chain (VB8.2); H-2 class II…
- UniProt
- P14434, P14483
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | J809.B5 TCR V alpha chain (VA2.8) | protein | 199 | 5% helix, 47% strand | — |
| B | J809.B5 TCR V beta chain (VB8.2) | protein | 239 | 8% helix, 52% strand | — |
| C | H-2 class II histocompatibility antigen, a-B alpha chain | protein | 179 | 15% helix, 45% strand | P14434 |
| D | 3K peptide and MHC iab beta CHAIN,H-2 class II histocompatibility antigen, a beta chain | protein | 200 | 19% helix, 44% strand | P14483 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.71 | 0.75 | 78 | empty |
| 2 | 216 | 0.56 | 0.79 | 26 | empty |
| 3 | 156 | 0.47 | 0.77 | 24 | empty |
| 4 | 186 | 0.47 | 0.75 | 26 | empty |
| 5 | 109 | 0.45 | 0.78 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2925 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2038 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 432 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 198 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4P23 · J809.B5 TCR bound to IAb/3K · the same entry in another collection · chain A against A, TM-score 1.00
- P14434 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-B alpha… · a predicted model of the same protein · chain C against A, TM-score 0.96
- P14483 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a beta… · a predicted model of the same protein · chain D against A, TM-score 0.73
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 P14434
- Every structure of UniProt P14483
- Elsewhere: RCSB PDB 4P23 · PDBe 4P23 · UniProt P14434 · UniProt P14483
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