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
- 4E41
- Type
- protein
- Length
- 1,589 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- EC
- 5.3.1.1
- UniProt
- P01903, P04229, P60174
- Ligands
- NA
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 179 | 20% helix, 45% strand | P04229 |
| C, H | Triosephosphate isomerase (EC 5.3.1.1) | protein | 15 | 0% helix, 13% strand | P60174 |
| D | T cell receptor G4 alpha chain | protein | 181 | 6% helix, 49% strand | — |
| E | T cell receptor G4 beta chain | protein | 236 | 6% helix, 52% strand | — |
| G | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 177 | 20% helix, 45% strand | P04229 |
| I | T cell receptor G4 alpha chain | protein | 190 | 5% helix, 50% strand | — |
| J | T cell receptor G4 beta chain | protein | 238 | 6% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, G, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.76 | 0.78 | 89 | NA |
| 2 | 974 | 0.74 | 0.77 | 78 | empty |
| 3 | 909 | 0.73 | 0.77 | 80 | empty |
| 4 | 116 | 0.52 | 0.81 | 27 | empty |
| 5 | 119 | 0.50 | 0.81 | 29 | empty |
Interfaces
23 interfaces between chains.
- A–B · 2541 Ų buried · 44 hydrogen bonds · protein-protein
- F–G · 2522 Ų buried · 41 hydrogen bonds · protein-protein
- I–J · 2217 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2191 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 664 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4E41 · Structural basis for the recognition of mutant self by a tumor-specific, MHC class… · the same entry in another collection · chain J against J, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P01903
- Every structure of UniProt P04229
- Every structure of UniProt P60174
- Elsewhere: RCSB PDB 4E41 · PDBe 4E41 · UniProt P01903 · UniProt P04229 · UniProt P60174
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