Research workbench
High resolution crystal structure of the MHC class I complex H- 2KB/VSV8
Analyse High resolution crystal structure of the MHC class I complex H- 2KB/VSV8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KPU
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- 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…
- UniProt
- P01901, P01887
- Ligands
- NAG, FUC
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 274 | 28% helix, 39% strand | P01901 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| P | Nucleocapsid | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.60 | 0.79 | 42 | MPD |
| 2 | 274 | 0.55 | 0.76 | 27 | empty |
| 3 | 67 | 0.52 | 0.86 | 17 | empty |
| 4 | 114 | 0.49 | 0.81 | 23 | empty |
| 5 | 98 | 0.41 | 0.77 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1374 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 927 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1KPU · High resolution crystal structure of the MHC class I complex H-2Kb/VSV8 · the same entry in another collection · chain A against A, 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 0.96
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
- Elsewhere: RCSB PDB 1KPU · PDBe 1KPU · UniProt P01901 · UniProt P01887
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