Research workbench
Structure of minor histocompatibility antigen peptide, H13B, complexed to H2-db
Analyse Structure of minor histocompatibility antigen peptide, H13B, complexed to H2-db in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JUF
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H2-db major histocompatibility antigen; Beta-2-microglobulin; H13B peptide
- UniProt
- P01899, P01887, Q9D8V0
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H2-db major histocompatibility antigen | protein | 276 | 26% helix, 39% strand | P01899 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C | H13B peptide | protein | 9 | 0% helix, 0% strand | Q9D8V0 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.64 | 0.76 | 55 | empty |
| 2 | 175 | 0.46 | 0.75 | 28 | empty |
| 3 | 98 | 0.41 | 0.77 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1330 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1JUF · Structure of Minor Histocompatibility Antigen peptide, H13b, complexed to H2-Db · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9D8V0 · AlphaFold monomer V2.0 prediction for minor histocompatibility antigen H13 (Q9D8V0) · a predicted model of the same protein · chain C against A, TM-score 0.35
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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt Q9D8V0
- Elsewhere: RCSB PDB 1JUF · PDBe 1JUF · UniProt P01899 · UniProt P01887 · UniProt Q9D8V0
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