Research workbench
Tap-a-associated rat MHC class I molecule
Analyse Tap-a-associated rat MHC class I molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KJM
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RT1 class I histocompatibility antigen, aa alpha chain, heavy chain…
- UniProt
- P16391, P07151
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RT1 class I histocompatibility antigen, aa alpha chain, heavy chain | protein | 277 | 26% helix, 39% strand | P16391 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 48% strand | P07151 |
| P | B6 peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.69 | 0.77 | 51 | empty |
| 2 | 121 | 0.49 | 0.80 | 28 | empty |
| 3 | 70 | 0.45 | 0.82 | 18 | empty |
| 4 | 69 | 0.44 | 0.82 | 18 | empty |
| 5 | 57 | 0.31 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1255 Ų buried · 17 hydrogen bonds · protein-protein
- A–P · 854 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1KJM · TAP-A-associated rat MHC class I molecule · the same entry in another collection · chain A against A, TM-score 1.00
- P16391 · AlphaFold monomer V2.0 prediction for RT1 class I histocompatibility antigen, aa alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P07151 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P07151) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P16391
- Every structure of UniProt P07151
- Elsewhere: RCSB PDB 1KJM · PDBe 1KJM · UniProt P16391 · UniProt P07151
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