MolNFT v1 · #93425 · protein
TCR interaction with peptide mimics of nickel offers structure insights to nickel contact allergy
4H25 · HLA class II histocompatibility antigen, dr alpha chain: “TCR interaction with peptide mimics of nickel offers structure insights to nickel contact allergy”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.62).…
- 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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