Research workbench
Crystal structure of the murine class I major histocompatibility complex of H-2KB, B2-microglobulin, and a 9-residue immunodominant peptide epitope GP33 derived from lcmv
Analyse Crystal structure of the murine class I major histocompatibility complex of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N59
- Type
- protein
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; Nonameric…
- UniProt
- P01901, P01887, Q9QDK7
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 276 | 26% helix, 41% strand | P01901 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 54% strand | P01887 |
| P, Q | Nonameric peptide, GP33 derived from lymphocytic choriomeningitis virus | protein | 8 | 0% helix, 0% strand | Q9QDK7 |
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.65 | 0.81 | 46 | empty |
| 2 | 338 | 0.61 | 0.78 | 39 | empty |
| 3 | 255 | 0.61 | 0.80 | 37 | empty |
| 4 | 222 | 0.59 | 0.80 | 33 | empty |
| 5 | 210 | 0.56 | 0.79 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1374 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1373 Ų buried · 28 hydrogen bonds · protein-protein
- A–P · 853 Ų buried · 13 hydrogen bonds · protein-protein
- C–Q · 834 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 792 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1N59 · Crystal structure of the Murine class I Major Histocompatibility Complex of H-2KB… · the same entry in another collection · chain D against D, TM-score 1.00
- P01901 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt Q9QDK7
- Elsewhere: RCSB PDB 1N59 · PDBe 1N59 · UniProt P01901 · UniProt P01887 · UniProt Q9QDK7
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