Research workbench
Crystal structure of the JM22 TCR in complex with HLA-A*0201 in complex with M1-F5L
Analyse Crystal structure of the JM22 TCR in complex with HLA-A*0201 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HHM
- Type
- protein
- Length
- 1,508 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; M1-F5L…
- UniProt
- P01892, P61769
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 212 | 32% helix, 31% strand | P01892 |
| B, G | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C, H | M1-F5L, gilglvftl | protein | 9 | 0% helix, 0% strand | — |
| D | JM22 TCR alpha chain | protein | 194 | 2% helix, 46% strand | — |
| E, J | JM22 TCR beta chain | protein | 240 | 6% helix, 48% strand | — |
| I | JM22 TCR alpha chain | protein | 196 | 3% helix, 45% strand | — |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.73 | 0.76 | 91 | empty |
| 2 | 1150 | 0.73 | 0.76 | 94 | empty |
| 3 | 768 | 0.71 | 0.77 | 72 | empty |
| 4 | 575 | 0.68 | 0.78 | 50 | empty |
| 5 | 177 | 0.46 | 0.75 | 36 | empty |
Interfaces
15 interfaces between chains.
- I–J · 2151 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2149 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1281 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1270 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 839 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5HHM · Crystal Structure of the JM22 TCR in complex with HLA-A*0201 in complex with M1-F5L · the same entry in another collection · chain J against J, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5HHM · PDBe 5HHM · UniProt P01892 · UniProt P61769
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