MolNFT v1 · #120206 · protein
Mouse MHC class I H-2KD with a MERS-cov-derived peptide 142-5
5GSV · H-2 class I histocompatibility antigen, K-D alpha chain: “Mouse MHC class I H-2KD with a MERS-cov-derived peptide 142-5”. X-ray diffraction, 5 pockets (best druggability 0.66). MolNFT v1 #120206 on GenesisL1: 3D structure, binding…
- PDB
- 5GSV
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- 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
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-D alpha chain | protein | 274 | 26% helix, 41% strand | P01902 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C | 10-mer peptide from spike protein | protein | 10 | 0% helix, 0% strand | A0A0U2P195 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.66 | 0.78 | 48 | empty |
| 2 | 99 | 0.47 | 0.80 | 17 | empty |
| 3 | 70 | 0.37 | 0.78 | 15 | empty |
| 4 | 64 | 0.30 | 0.75 | 16 | empty |
| 5 | 57 | 0.27 | 0.73 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1389 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1055 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5GSV · Mouse MHC class I H-2Kd with a MERS-CoV-derived peptide 142-5 · the same entry in another collection · chain A against A, 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 0.98
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 5GSV · PDBe 5GSV · UniProt P01902 · UniProt P61769 · UniProt A0A0U2P195
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