Research workbench
UL40:01 TCR in complex with HLA-E with a non-natural amino acid
Analyse UL40:01 TCR in complex with HLA-E with a non-natural amino acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NDT
- Type
- protein
- Length
- 1,617 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.999
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, alpha chain E; Beta-2-microglobulin; UL40(15-23…
- UniProt
- P13747, P61769, A0A087WT03, A0A087X096, P01848, A0A5B0, A0A0B4J200, A0A5B9
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.999 · 8 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | HLA class I histocompatibility antigen, alpha chain E | protein | 271 | 28% helix, 39% strand | P13747 |
| BBB, GGG | Beta-2-microglobulin | protein | 99 | 0% helix, 51% strand | P61769 |
| CCC, HHH | UL40(15-23 H4C) | protein | 9 | 0% helix, 0% strand | — |
| DDD | T cell receptor alpha variable 26-1,T cell receptor alpha joining 37,T cell receptor alpha chain constant | protein | 190 | 3% helix, 42% strand | A0A087WT03, A0A087X096, P01848 |
| EEE | T cell receptor beta variable 14,T cell receptor beta joining 2-3,T cell receptor beta constant 2 | protein | 240 | 7% helix, 49% strand | A0A5B0, A0A0B4J200, A0A5B9 |
| FFF | HLA class I histocompatibility antigen, alpha chain E | protein | 270 | 27% helix, 37% strand | P13747 |
| III | T cell receptor alpha variable 26-1,T cell receptor alpha joining 37,T cell receptor alpha chain constant | protein | 189 | 3% helix, 44% strand | A0A087WT03, A0A087X096, P01848 |
| JJJ | T cell receptor beta variable 14,T cell receptor beta joining 2-3,T cell receptor beta constant 2 | protein | 241 | 7% helix, 49% strand | A0A5B0, A0A0B4J200, A0A5B9 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.78 | 0.82 | 79 | empty |
| 2 | 924 | 0.78 | 0.81 | 86 | empty |
| 3 | 1062 | 0.70 | 0.75 | 92 | empty |
| 4 | 659 | 0.69 | 0.77 | 54 | empty |
| 5 | 640 | 0.69 | 0.77 | 56 | empty |
Interfaces
20 interfaces between chains.
- DDD–EEE · 2108 Ų buried · 28 hydrogen bonds · protein-protein
- III–JJJ · 2095 Ų buried · 26 hydrogen bonds · protein-protein
- FFF–GGG · 1316 Ų buried · 21 hydrogen bonds · protein-protein
- AAA–BBB · 1298 Ų buried · 21 hydrogen bonds · protein-protein
- AAA–CCC · 915 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain GGG against A, TM-score 0.98
- P13747 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain AAA against A, TM-score 0.97
- A0A5B9 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 2 (A0A5B9) · a predicted model of the same protein · chain JJJ 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 DDD against A, TM-score 0.41
- A0A5B0 · AlphaFold monomer V2.0 prediction for T cell receptor beta variable 14 (A0A5B0) · a predicted model of the same protein · chain JJJ against A, TM-score 0.39
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 P13747
- Every structure of UniProt P61769
- Every structure of UniProt A0A087WT03
- Every structure of UniProt A0A087X096
- Every structure of UniProt P01848
- Every structure of UniProt A0A5B0
- Every structure of UniProt A0A0B4J200
- Every structure of UniProt A0A5B9
- Elsewhere: RCSB PDB 7NDT · PDBe 7NDT · UniProt P13747 · UniProt P61769 · UniProt A0A087WT03 · UniProt A0A087X096 · UniProt P01848 · UniProt A0A5B0 · UniProt A0A0B4J200 · UniProt A0A5B9
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