MolNFT v1 · #20606 · protein
MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and herpes simplex virus glycoprotein B peptide
1RJY · H-2 class I histocompatibility antigen, K-B alpha chain: “MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and herpes simplex virus…”. X-ray diffraction, 9 pockets (best druggability 0.65). MolNFT…
- PDB
- 1RJY
- Type
- protein
- Length
- 772 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…
- UniProt
- P01901, P01887, P06436
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 27% helix, 40% strand | P01901 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01887 |
| P, Q | Glycoprotein B | protein | 8 | 0% helix, 0% strand | P06436 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.65 | 0.75 | 55 | empty |
| 2 | 667 | 0.65 | 0.75 | 59 | empty |
| 3 | 176 | 0.55 | 0.80 | 36 | empty |
| 4 | 159 | 0.52 | 0.79 | 32 | empty |
| 5 | 68 | 0.45 | 0.82 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1258 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1253 Ų buried · 22 hydrogen bonds · protein-protein
- D–Q · 877 Ų buried · 15 hydrogen bonds · protein-protein
- A–P · 876 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 184 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1RJY · Mhc Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and… · the same entry in another collection · chain Q against Q, 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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt P06436
- Elsewhere: RCSB PDB 1RJY · PDBe 1RJY · UniProt P01901 · UniProt P01887 · UniProt P06436
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