MolNFT v1 · #20608 · protein
MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and herpes simplex virus glycoprotein B peptide
1RK0 · H-2 class I histocompatibility antigen, K-B alpha chain: “MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and herpes simplex virus glycoprotein B…”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability…
- PDB
- 1RK0
- 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, P06436
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 274 | 28% helix, 40% strand | P01901 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| P | Glycoprotein B | protein | 8 | 0% helix, 0% strand | P06436 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.61 | 0.80 | 38 | empty |
| 2 | 345 | 0.58 | 0.76 | 36 | empty |
| 3 | 68 | 0.53 | 0.86 | 18 | empty |
| 4 | 146 | 0.49 | 0.78 | 23 | empty |
| 5 | 93 | 0.43 | 0.79 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1340 Ų buried · 23 hydrogen bonds · protein-protein
- A–P · 815 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1RK0 · Mhc Class I H-2Kb Heavy Chain Complexed With beta-2 Microglobulin and Herpes Simplex… · 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 0.97
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 P06436
- Elsewhere: RCSB PDB 1RK0 · PDBe 1RK0 · UniProt P01901 · UniProt P01887 · UniProt P06436
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