Research workbench
Crystal structure of the 2B4 TCR in complex with 2A/I-Ek
Analyse Crystal structure of the 2B4 TCR in complex with 2A/I-Ek in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P2O
- Type
- protein
- Length
- 815 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.603
- Source
- Mus musculus; synthetic construct
- Molecule
- H-2 class II histocompatibility antigen, E-K alpha chain; MHC class II E-beta-k; 2B4…
- UniProt
- P04224, Q31163
- Ligands
- NAG, FUC
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.603 · 5 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class II histocompatibility antigen, E-K alpha chain | protein | 175 | 14% helix, 49% strand | P04224 |
| B | MHC class II E-beta-k | protein | 176 | 17% helix, 45% strand | Q31163 |
| C | 2B4 T-cell receptor alpha chain | protein | 200 | 5% helix, 51% strand | — |
| D | 2B4 T-cell receptor beta chain | protein | 244 | 8% helix, 50% strand | — |
| P | 2A peptide | protein | 20 | 0% helix, 10% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.70 | 0.75 | 69 | empty |
| 2 | 158 | 0.44 | 0.75 | 25 | empty |
| 3 | 60 | 0.32 | 0.77 | 18 | empty |
| 4 | 80 | 0.31 | 0.73 | 22 | empty |
| 5 | 72 | 0.30 | 0.74 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2452 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2179 Ų buried · 34 hydrogen bonds · protein-protein
- A–P · 756 Ų buried · 14 hydrogen bonds · protein-protein
- B–P · 652 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4P2O · Crystal structure of the 2B4 TCR in complex with 2A/I-ek · the same entry in another collection · chain A against A, 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 0.97
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 Q31163
- Elsewhere: RCSB PDB 4P2O · PDBe 4P2O · UniProt P04224 · UniProt Q31163
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