Research workbench
Structure of HLA-A2 in complex with an altered peptide ligands based on mart-1 variant epitope
Analyse Structure of HLA-A2 in complex with an altered peptide ligands based on mart-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WJ5
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Melanoma…
- UniProt
- P01892, P61769, Q16655
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 28% helix, 40% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Melanoma antigen recognized by T-cells 1 | protein | 10 | 0% helix, 0% strand | Q16655 |
Ligands and binding sites
- GOL · Glycerol · additive · 13 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.69 | 0.78 | 54 | GOL |
| 2 | 607 | 0.68 | 0.77 | 62 | GOL |
| 3 | 619 | 0.65 | 0.76 | 74 | empty |
| 4 | 460 | 0.63 | 0.77 | 54 | empty |
| 5 | 64 | 0.38 | 0.79 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1437 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1389 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 921 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 914 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 150 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 modified (disulfide, nonstandard).
Compared structures
- 4WJ5 · Structure of HLA-A2 in complex with an altered peptide ligands based on Mart-1 variant… · the same entry in another collection · chain C against C, 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
- Q16655 · AlphaFold monomer V2.0 prediction for melanoma antigen recognized by T-cells 1 (Q16655) · a predicted model of the same protein · chain C against A, TM-score 0.32
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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt Q16655
- Elsewhere: RCSB PDB 4WJ5 · PDBe 4WJ5 · UniProt P01892 · UniProt P61769 · UniProt Q16655
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