Research workbench
Evidence that structural rearrangements AND/OR flexibility during TCR binding can contribute to T-cell activation
Analyse Evidence that structural rearrangements AND/OR flexibility during TCR binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R5V
- Type
- protein
- Length
- 756 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, E-K alpha chain; Artificial peptide; MHC…
- UniProt
- P04224, P18468
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | H-2 class II histocompatibility antigen, E-K alpha chain | protein | 180 | 15% helix, 48% strand | P04224 |
| E, F | Artificial peptide | protein | 13 | 0% helix, 15% strand | — |
| B, D | MHC H2-ie-beta | protein | 185 | 19% helix, 44% strand | P18468 |
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 | 615 | 0.71 | 0.79 | 46 | empty |
| 2 | 680 | 0.69 | 0.77 | 72 | empty |
| 3 | 183 | 0.48 | 0.76 | 22 | empty |
| 4 | 192 | 0.46 | 0.75 | 33 | empty |
| 5 | 143 | 0.43 | 0.75 | 21 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2494 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2464 Ų buried · 41 hydrogen bonds · protein-protein
- C–F · 680 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 673 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 596 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1R5V · Evidence that structural rearrangements and/or flexibility during TCR binding can… · the same entry in another collection · chain D against D, TM-score 1.00
- P04224 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, E-K alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P18468 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, I-a beta… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P04224
- Every structure of UniProt P18468
- Elsewhere: RCSB PDB 1R5V · PDBe 1R5V · UniProt P04224 · UniProt P18468
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