Research workbench
Structure determination of an enhanced affinity TCR, A24B17, in complex with HLA-A*02:01 presenting a mart-1 peptide, eaagigiltv
Analyse Structure determination of an enhanced affinity TCR, A24B17, 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
- 6TMO
- Type
- protein
- Length
- 827 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Eaagigiltv; Alpha chain of engineered high…
- UniProt
- A0A5B8RNS7, P61769
- Ligands
- TAM, SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 27% helix, 38% strand | A0A5B8RNS7 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Eaagigiltv | protein | 10 | 0% helix, 10% strand | — |
| D | Alpha chain of engineered high affinity T-cell receptor | protein | 197 | 5% helix, 45% strand | — |
| E | Beta chain of high affinity engineered T-cell receptor | protein | 244 | 7% helix, 53% strand | — |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 3 copies · chains A, D, E
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, E
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, D, B, E
- GOL · Glycerol · additive · 5 copies · chains A, D, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.70 | 0.74 | 98 | EDO, TAM |
| 2 | 552 | 0.68 | 0.78 | 53 | GOL, EDO |
| 3 | 106 | 0.43 | 0.78 | 20 | empty |
| 4 | 88 | 0.43 | 0.79 | 14 | GOL |
| 5 | 103 | 0.42 | 0.78 | 19 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2133 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1359 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 875 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 572 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 545 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6TMO · Structure determination of an enhanced affinity TCR, a24b17, in complex with HLA-A*02:01… · the same entry in another collection · chain A against A, 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
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 A0A5B8RNS7
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6TMO · PDBe 6TMO · UniProt A0A5B8RNS7 · UniProt P61769
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