MolNFT v1 · #108654 · protein
Weak TCR binding to an unstable insulin epitope drives type 1 diabetes
4WDI · 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), 11 pockets (best druggability 0.79). MolNFT v1 #108654 on…
- PDB
- 4WDI
- Type
- protein
- Length
- 772 residues
- Chains
- 6
- 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
- P61769, P01308
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, K-D alpha chain | protein | 277 | 27% helix, 39% strand | — |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Insulin | protein | 9 | 0% helix, 0% strand | P01308 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.79 | 0.81 | 115 | SO4 |
| 2 | 287 | 0.65 | 0.81 | 36 | empty |
| 3 | 176 | 0.48 | 0.76 | 31 | empty |
| 4 | 145 | 0.47 | 0.78 | 23 | empty |
| 5 | 99 | 0.47 | 0.80 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1349 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1346 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 954 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 498 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4WDI · Weak TCR binding to an unstable insulin epitope drives type 1 diabetes · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B 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 P61769
- Every structure of UniProt P01308
- Elsewhere: RCSB PDB 4WDI · PDBe 4WDI · UniProt P61769 · UniProt P01308
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