Research workbench
Crystal structure of a single chain trimer composed of the MHC 1 heavy chain H2-kb wt, beta-2MICROGLOBULIN, and ovalbumin derived peptide
Analyse Crystal structure of a single chain trimer composed of the MHC 1 heavy chain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OQF
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-MICROGLOBULIN,H-2 class I histocompatibility antigen, K-B alpha chain
- UniProt
- P01887, P01901
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-2-MICROGLOBULIN,H-2 class I histocompatibility antigen, K-B alpha chain | protein | 388 | 20% helix, 40% strand | P01887, P01901 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.63 | 0.74 | 59 | empty |
| 2 | 601 | 0.63 | 0.74 | 58 | empty |
| 3 | 204 | 0.55 | 0.79 | 33 | empty |
| 4 | 204 | 0.54 | 0.78 | 39 | empty |
| 5 | 78 | 0.47 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 182 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5OQF · Crystal structure of a single chain trimer composed of the MHC 1 heavy chain H2-Kb WT… · 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 0.26
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 P01887
- Every structure of UniProt P01901
- Elsewhere: RCSB PDB 5OQF · PDBe 5OQF · UniProt P01887 · UniProt P01901
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