Research workbench
Structural basis for the recognition of mutant self by a tumor- specific, MHC class II-restricted T cell receptor G4
Analyse Structural basis for the recognition of mutant self by a tumor- specific, MHC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E42
- Type
- protein
- Length
- 829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor G4 alpha chain; T cell receptor G4 beta chain
- Ligands
- NA, CL, NO3
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T cell receptor G4 alpha chain | protein | 187 | 5% helix, 48% strand | — |
| B | T cell receptor G4 beta chain | protein | 231 | 7% helix, 53% strand | — |
| C | T cell receptor G4 alpha chain | protein | 182 | 5% helix, 48% strand | — |
| D | T cell receptor G4 beta chain | protein | 229 | 6% helix, 52% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · 9 copies · chains A, B, D
- NO3 · Nitrate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.80 | 0.82 | 99 | CL, NA |
| 2 | 536 | 0.76 | 0.83 | 51 | empty |
| 3 | 989 | 0.75 | 0.78 | 71 | NA |
| 4 | 120 | 0.48 | 0.79 | 16 | CL |
| 5 | 71 | 0.35 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2163 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2059 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 529 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 138 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 134 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4E42 · Structural basis for the recognition of mutant self by a tumor-specific, MHC class… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4E42 · PDBe 4E42
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