Research workbench
Crystal structure of the murine class I major histocompatibility complex H-2DB in complex with lcmv-derived GP33 altered peptide ligand V3P
Analyse Crystal structure of the murine class I major histocompatibility complex H-2DB… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NSK
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin…
- UniProt
- P01899, P01887
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 274 | 26% helix, 39% strand | P01899 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P01887 |
| C | Pre-glycoprotein polyprotein gp | protein | 9 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.66 | 0.76 | 55 | empty |
| 2 | 161 | 0.51 | 0.78 | 33 | empty |
| 3 | 77 | 0.43 | 0.80 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1216 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 920 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4NSK · CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX… · 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
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
- Elsewhere: RCSB PDB 4NSK · PDBe 4NSK · UniProt P01899 · UniProt P01887
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