Research workbench
Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR
Analyse Structural basis for recognition of mutant self by a tumor-specific, MHC class… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IAM
- Type
- protein
- Length
- 813 residues
- Chains
- 5
- 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, P01848, P01850
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 15% helix, 45% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 182 | 15% helix, 47% strand | P04229 |
| P | 15-mer peptide from triosephosphate isomerase (EC 5.3.1.1) | protein | 15 | 0% helix, 13% strand | P60174 |
| C | CD4+ T cell receptor E8 alpha chain | protein | 198 | 5% helix, 48% strand | P01848 |
| D | CD4+ T cell receptor E8 beta chain | protein | 239 | 8% helix, 51% strand | P01850 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.74 | 0.77 | 89 | empty |
| 2 | 163 | 0.50 | 0.78 | 30 | empty |
| 3 | 187 | 0.47 | 0.75 | 26 | empty |
| 4 | 107 | 0.38 | 0.75 | 17 | empty |
| 5 | 53 | 0.32 | 0.77 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2538 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2255 Ų buried · 26 hydrogen bonds · protein-protein
- A–P · 693 Ų buried · 13 hydrogen bonds · protein-protein
- B–P · 575 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 455 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2IAM · Structural basis for recognition of mutant self by a tumor-specific, MHC class… · the same entry in another collection · chain D against D, 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
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain D against A, TM-score 0.54
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain C against A, TM-score 0.44
- P60174 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P60174) · a predicted model of the same protein · chain P against A, TM-score 0.22
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
- Every structure of UniProt P01848
- Every structure of UniProt P01850
- Elsewhere: RCSB PDB 2IAM · PDBe 2IAM · UniProt P01903 · UniProt P04229 · UniProt P60174 · UniProt P01848 · UniProt P01850
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