Research workbench
TCR interaction with peptide mimics of nickel offers structure insights to nickel contact allergy
Analyse TCR interaction with peptide mimics of nickel offers structure insights to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H25
- Type
- protein
- Length
- 774 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; MHC class II antigen; Peptide
- UniProt
- P01903, B8YAC7
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 14% helix, 47% strand | P01903 |
| B | MHC class II antigen | protein | 188 | 19% helix, 45% strand | B8YAC7 |
| C, F | Peptide | protein | 22 | 0% helix, 5% strand | — |
| E | MHC class II antigen | protein | 182 | 19% helix, 46% strand | B8YAC7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, D, E
- IPA · Isopropyl alcohol · additive · 4 copies · chains A, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.62 | 0.75 | 46 | IPA |
| 2 | 77 | 0.48 | 0.83 | 23 | empty |
| 3 | 198 | 0.48 | 0.75 | 30 | IPA |
| 4 | 204 | 0.46 | 0.74 | 34 | empty |
| 5 | 177 | 0.45 | 0.74 | 21 | empty |
Interfaces
10 interfaces between chains.
- D–E · 2484 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2455 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 867 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 836 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 760 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4H25 · TCR interaction with peptide mimics of nickel offers structure insights to nickel contact… · the same entry in another collection · chain F against F, 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 B8YAC7
- Elsewhere: RCSB PDB 4H25 · PDBe 4H25 · UniProt P01903 · UniProt B8YAC7
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