Research workbench
Crystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 antigen peptide
Analyse Crystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 antigen peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JZI
- Type
- protein
- Length
- 1,634 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; Klv…
- UniProt
- P01892, P61769
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 260 | 25% helix, 31% strand | P01892 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 42% strand | P61769 |
| C, H | Klv peptide | protein | 10 | 0% helix, 0% strand | — |
| F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 262 | 25% helix, 32% strand | P01892 |
| G | Beta-2-microglobulin | protein | 98 | 0% helix, 44% strand | P61769 |
| D | HCV1406 TCR alpha chain | protein | 207 | 1% helix, 43% strand | — |
| E | HCV1406 TCR beta chain | protein | 240 | 7% helix, 48% strand | — |
| I | HCV1406 TCR alpha chain | protein | 207 | 1% helix, 44% strand | — |
| J | HCV1406 TCR beta chain | protein | 241 | 7% helix, 47% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.86 | 0.87 | 123 | empty |
| 2 | 534 | 0.75 | 0.83 | 52 | empty |
| 3 | 451 | 0.74 | 0.83 | 53 | empty |
| 4 | 709 | 0.71 | 0.77 | 60 | empty |
| 5 | 630 | 0.69 | 0.78 | 63 | empty |
Interfaces
20 interfaces between chains.
- I–J · 2725 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2681 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1330 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 883 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5JZI · Crystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 antigen peptide · 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 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5JZI · PDBe 5JZI · UniProt P01892 · UniProt P61769
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