Research workbench
Mouse MHC class I H-2KD with a MERS-cov-derived peptide I5A
Analyse Mouse MHC class I H-2KD with a MERS-cov-derived peptide I5A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GSR
- Type
- protein
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin; H-2 class I histocompatibility antigen, K-D alpha chain; 9-mer…
- UniProt
- P61769, P01902, A0A0U2W1D8
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| A, C | H-2 class I histocompatibility antigen, K-D alpha chain | protein | 274 | 26% helix, 41% strand | P01902 |
| P, Q | 9-mer peptide from spike protein | protein | 9 | 0% helix, 0% strand | A0A0U2W1D8 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.77 | 0.79 | 81 | empty |
| 2 | 652 | 0.70 | 0.78 | 56 | empty |
| 3 | 653 | 0.70 | 0.78 | 53 | empty |
| 4 | 141 | 0.50 | 0.79 | 22 | empty |
| 5 | 185 | 0.48 | 0.76 | 28 | empty |
Interfaces
7 interfaces between chains.
- B–A · 1432 Ų buried · 15 hydrogen bonds · protein-protein
- D–C · 1399 Ų buried · 15 hydrogen bonds · protein-protein
- C–Q · 975 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 960 Ų buried · 19 hydrogen bonds · protein-protein
- D–A · 371 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5GSR · Mouse MHC class I H-2Kd with a MERS-CoV-derived peptide I5A · the same entry in another collection · chain Q against Q, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P01902 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-D alpha… · a predicted model of the same protein · chain A 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 P61769
- Every structure of UniProt P01902
- Every structure of UniProt A0A0U2W1D8
- Elsewhere: RCSB PDB 5GSR · PDBe 5GSR · UniProt P61769 · UniProt P01902 · UniProt A0A0U2W1D8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.