MolNFT v1 · #182178 · protein
HLA-A*02:01 bound to neuroblastoma derived IGFBPL1 peptide
7MJ7 · MHC class I antigen: “HLA-A*02:01 bound to neuroblastoma derived IGFBPL1 peptide”. X-ray diffraction, 5 pockets (best druggability 0.67). MolNFT v1 #182178 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MJ7
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Insulin-like growth factor-binding…
- UniProt
- Q861F7, P61769, Q8WX77
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 27% helix, 40% strand | Q861F7 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C | Insulin-like growth factor-binding protein-like 1 peptide | protein | 11 | 0% helix, 0% strand | Q8WX77 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 615 | 0.67 | 0.77 | 57 | GOL |
| 2 | 106 | 0.43 | 0.78 | 19 | empty |
| 3 | 50 | 0.39 | 0.82 | 16 | empty |
| 4 | 62 | 0.31 | 0.75 | 15 | empty |
| 5 | 50 | 0.30 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1198 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 844 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7MJ7 · HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide · 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
- Q8WX77 · AlphaFold monomer V2.0 prediction for insulin-like growth factor- binding protein-like 1… · a predicted model of the same protein · chain C against A, TM-score 0.36
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 Q861F7
- Every structure of UniProt P61769
- Every structure of UniProt Q8WX77
- Elsewhere: RCSB PDB 7MJ7 · PDBe 7MJ7 · UniProt Q861F7 · UniProt P61769 · UniProt Q8WX77
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