Research workbench
The crystal structure of LC13 TCR in complex with HLAB8-EBV peptide complex
Analyse The crystal structure of LC13 TCR in complex with HLAB8-EBV peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MI5
- Type
- protein
- Length
- 827 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC heavy chain; Beta 2 microglobulin; Epstein barr virus peptide; TCR alpha chain; TCR…
- UniProt
- P30460, P61769, P01848, P01850
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC heavy chain | protein | 277 | 24% helix, 38% strand | P30460 |
| B | Beta 2 microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Epstein barr virus peptide | protein | 9 | 0% helix, 0% strand | — |
| D | TCR alpha chain | protein | 201 | 5% helix, 38% strand | P01848 |
| E | TCR beta chain | protein | 241 | 7% helix, 49% strand | P01850 |
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 | 1048 | 0.72 | 0.76 | 82 | empty |
| 2 | 490 | 0.66 | 0.78 | 58 | empty |
| 3 | 145 | 0.48 | 0.78 | 20 | empty |
| 4 | 72 | 0.40 | 0.79 | 17 | empty |
| 5 | 71 | 0.36 | 0.77 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2107 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1409 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1009 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 633 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 488 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1MI5 · The crystal structure of LC13 TcR in complex with HLAB8-EBV peptide complex · the same entry in another collection · chain E against E, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain E against A, TM-score 0.53
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain D against A, TM-score 0.44
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 P30460
- Every structure of UniProt P61769
- Every structure of UniProt P01848
- Every structure of UniProt P01850
- Elsewhere: RCSB PDB 1MI5 · PDBe 1MI5 · UniProt P30460 · UniProt P61769 · UniProt P01848 · UniProt P01850
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.