MolNFT v1 · #111983 · protein
Weak TCR binding to an unstable insulin epitope drives type 1 diabetes
4Z78 · H-2 class I histocompatibility antigen, K-D alpha chain: “Weak TCR binding to an unstable insulin epitope drives type 1 diabetes”. X-ray diffraction, 1 ligand (SO4), 18 pockets (best druggability 0.69). MolNFT v1 #111983 on…
- PDB
- 4Z78
- Type
- protein
- Length
- 1,161 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-D alpha chain; Beta-2-microglobulin; Insulin
- UniProt
- P01902, P61769, P01308
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | H-2 class I histocompatibility antigen, K-D alpha chain | protein | 277 | 28% helix, 39% strand | P01902 |
| B, E, H | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F, I | Insulin | protein | 10 | 0% helix, 0% strand | P01308 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, D, G, H, E
- GOL · Glycerol · additive · 6 copies · chains A, D, E, H, G
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.69 | 0.77 | 56 | empty |
| 2 | 625 | 0.68 | 0.77 | 56 | EDO |
| 3 | 532 | 0.67 | 0.77 | 44 | GOL |
| 4 | 235 | 0.51 | 0.75 | 40 | empty |
| 5 | 153 | 0.50 | 0.78 | 23 | EDO, SO4 |
Interfaces
11 interfaces between chains.
- D–E · 1418 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1370 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1357 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 998 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 991 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4Z78 · Weak TCR binding to an unstable insulin epitope drives type 1 diabetes · the same entry in another collection · chain I against I, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain H against A, TM-score 0.99
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 P01902
- Every structure of UniProt P61769
- Every structure of UniProt P01308
- Elsewhere: RCSB PDB 4Z78 · PDBe 4Z78 · UniProt P01902 · UniProt P61769 · UniProt P01308
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