Research workbench
6218 TCR in complex with H2DB pa with an engineered TCR-pmhc disulfide bond
Analyse 6218 TCR in complex with H2DB pa with an engineered TCR-pmhc disulfide bond in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N5C
- Type
- protein
- Length
- 818 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; Peptide…
- UniProt
- P01899, P61769, O89752, A0A075B6C4, K7N5N2, A0A0G2LB96, K7N5M4
- Ligands
- NA
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 274 | 28% helix, 39% strand | P01899 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Peptide from polymerase acidic protein | protein | 10 | 0% helix, 0% strand | O89752 |
| D | Fusion protein of T cell receptor alpha variable 21-DV12 with T-cell receptor, SP3.4 alpha chain | protein | 194 | 5% helix, 42% strand | A0A075B6C4, K7N5N2 |
| E | Fusion protein of T cell receptor beta, variable 29 and human nkt TCR beta chain | protein | 240 | 6% helix, 49% strand | A0A0G2LB96, K7N5M4 |
Ligands and binding sites
- NA · Sodium ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.71 | 0.75 | 76 | empty |
| 2 | 598 | 0.66 | 0.76 | 56 | empty |
| 3 | 133 | 0.46 | 0.77 | 24 | empty |
| 4 | 84 | 0.38 | 0.77 | 17 | empty |
| 5 | 90 | 0.34 | 0.74 | 22 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2176 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1394 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 902 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 362 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 310 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 7N5C · 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond · 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 P01899
- Every structure of UniProt P61769
- Every structure of UniProt O89752
- Every structure of UniProt A0A075B6C4
- Every structure of UniProt K7N5N2
- Every structure of UniProt A0A0G2LB96
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 7N5C · PDBe 7N5C · UniProt P01899 · UniProt P61769 · UniProt O89752 · UniProt A0A075B6C4 · UniProt K7N5N2 · UniProt A0A0G2LB96 · UniProt K7N5M4
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