MolNFT v1 · #20609 · protein
MHC class I natural H-2KB heavy chain complexed with beta-2 microglobulin and herpes simplex virus mutant glycoprotein B peptide
1RK1 · H-2 class I histocompatibility antigen, K-B alpha chain: “MHC class I natural H-2KB heavy chain complexed with beta-2 microglobulin and herpes simplex virus mutant…”. X-ray diffraction, 2 ligands (NAG, FUL), 5 pockets (best…
- PDB
- 1RK1
- 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, FUL
- Pockets
- 5 · best druggability 0.59
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 · 2 copies · chains A
- FUL · beta-L-fucopyranose · 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 | 238 | 0.59 | 0.80 | 31 | empty |
| 2 | 334 | 0.57 | 0.76 | 39 | empty |
| 3 | 69 | 0.52 | 0.86 | 18 | empty |
| 4 | 120 | 0.48 | 0.80 | 22 | empty |
| 5 | 79 | 0.42 | 0.79 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1342 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 833 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1RK1 · Mhc Class I Natural H-2Kb Heavy Chain Complexed With beta-2 Microglobulin and Herpes… · 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 1RK1 · PDBe 1RK1 · UniProt P01901 · UniProt P01887 · UniProt P06436
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