Research workbench
Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid
Analyse Gag:02 TCR in complex with HLA-E featuring 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
- 7NDU
- Type
- protein
- Length
- 810 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, alpha chain E; Beta-2-microglobulin…
- UniProt
- P13747, P61769, A0A0B4J268, A0A075B6U7, P0DSE1, P04435, A0A0J9YX06, K7N5M4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.9 · 5 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | HLA class I histocompatibility antigen, alpha chain E | protein | 276 | 26% helix, 38% strand | P13747 |
| BBB | Beta-2-microglobulin | protein | 100 | 0% helix, 44% strand | P61769 |
| CCC | Gag6V(276-284 H4C) | protein | 9 | 0% helix, 0% strand | — |
| DDD | T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain | protein | 184 | 2% helix, 40% strand | A0A0B4J268, A0A075B6U7, P0DSE1 |
| EEE | T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain | protein | 241 | 6% helix, 49% strand | P04435, A0A0J9YX06, K7N5M4 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.72 | 0.76 | 76 | empty |
| 2 | 717 | 0.69 | 0.76 | 64 | empty |
| 3 | 276 | 0.66 | 0.82 | 43 | empty |
| 4 | 105 | 0.50 | 0.81 | 22 | empty |
| 5 | 51 | 0.45 | 0.85 | 18 | empty |
Interfaces
7 interfaces between chains.
- DDD–EEE · 2158 Ų buried · 37 hydrogen bonds · protein-protein
- AAA–BBB · 1377 Ų buried · 23 hydrogen bonds · protein-protein
- AAA–CCC · 921 Ų buried · 20 hydrogen bonds · protein-protein
- AAA–EEE · 513 Ų buried · 8 hydrogen bonds · protein-protein
- AAA–DDD · 491 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain BBB 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 0.94
- P0DSE1 · AlphaFold monomer V2.0 prediction for M1-specific T cell receptor alpha chain (P0DSE1) · a predicted model of the same protein · chain DDD against A, TM-score 0.65
- P04435 · AlphaFold monomer V2.0 prediction for T cell receptor beta variable 7-9 (P04435) · a predicted model of the same protein · chain EEE against A, TM-score 0.38
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 A0A0B4J268
- Every structure of UniProt A0A075B6U7
- Every structure of UniProt P0DSE1
- Every structure of UniProt P04435
- Every structure of UniProt A0A0J9YX06
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 7NDU · PDBe 7NDU · UniProt P13747 · UniProt P61769 · UniProt A0A0B4J268 · UniProt A0A075B6U7 · UniProt P0DSE1 · UniProt P04435 · UniProt A0A0J9YX06 · UniProt K7N5M4
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