MolNFT v1 · #182217 · protein
Human leukocyte antigen A*0201 in complex with SARS-cov-2 epitope ylqprtfll
7MKB · MHC class I antigen: “Human leukocyte antigen A*0201 in complex with SARS-cov-2 epitope ylqprtfll”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #182217 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7MKB
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Spike protein S1
- UniProt
- U5YJM1, P61769, P0DTC2
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 274 | 28% helix, 39% strand | U5YJM1 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Spike protein S1 | protein | 9 | 0% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.68 | 0.78 | 59 | GOL |
| 2 | 152 | 0.44 | 0.76 | 29 | GOL |
| 3 | 54 | 0.28 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1440 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 940 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7MKB · Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL · 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 0.98
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 U5YJM1
- Every structure of UniProt P61769
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7MKB · PDBe 7MKB · UniProt U5YJM1 · UniProt P61769 · UniProt P0DTC2
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