MolNFT v1 · #180957 · protein
Human leukocyte antigen A*0201 in complex with SARS-COV2 epitope alweiqqvv
7LG2 · MHC class I antigen: “Human leukocyte antigen A*0201 in complex with SARS-COV2 epitope alweiqqvv”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #180957 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7LG2
- 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; Non-structural protein 8
- UniProt
- U5YJM1, P61769, P0DTD1
- Pockets
- 4 · best druggability 0.67
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, 40% strand | U5YJM1 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Non-structural protein 8 | protein | 9 | 0% helix, 0% strand | P0DTD1 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, C, B
- PGE · Triethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.67 | 0.77 | 53 | GOL, PGE |
| 2 | 151 | 0.53 | 0.80 | 26 | GOL |
| 3 | 115 | 0.41 | 0.76 | 18 | empty |
| 4 | 59 | 0.31 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1422 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 910 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7LG2 · Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope ALWEIQQVV · 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 0.97
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 U5YJM1
- Every structure of UniProt P61769
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 7LG2 · PDBe 7LG2 · UniProt U5YJM1 · UniProt P61769 · UniProt P0DTD1
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