MolNFT v1 · #120208 · protein
Mouse MHC class I H-2KD with a MERS-cov-derived peptide 142-2
5GSX · H-2 class I histocompatibility antigen, K-D alpha chain: “Mouse MHC class I H-2KD with a MERS-cov-derived peptide 142-2”. X-ray diffraction, 10 pockets (best druggability 0.70). MolNFT v1 #120208 on GenesisL1: 3D structure, binding…
- PDB
- 5GSX
- Type
- protein
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-D alpha chain; Beta-2-microglobulin; 10-mer…
- UniProt
- P01902, P61769, A0A0U2P195
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, K-D alpha chain | protein | 274 | 27% helix, 39% strand | P01902 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | 10-mer peptide from spike protein | protein | 10 | 0% helix, 0% strand | A0A0U2P195 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.70 | 0.85 | 36 | empty |
| 2 | 605 | 0.68 | 0.77 | 54 | empty |
| 3 | 595 | 0.67 | 0.77 | 55 | empty |
| 4 | 206 | 0.49 | 0.76 | 24 | empty |
| 5 | 57 | 0.45 | 0.84 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1365 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1354 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1042 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1013 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 335 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5GSX · Mouse MHC class I H-2Kd with a MERS-CoV-derived peptide 142-2 · the same entry in another collection · chain F against F, TM-score 1.00
- 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 0.98
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P01902
- Every structure of UniProt P61769
- Every structure of UniProt A0A0U2P195
- Elsewhere: RCSB PDB 5GSX · PDBe 5GSX · UniProt P01902 · UniProt P61769 · UniProt A0A0U2P195
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.