Research workbench
Crystal structure of HLA-A0201 in complex with an azobenzene- containing peptide
Analyse Crystal structure of HLA-A0201 in complex with an azobenzene- containing peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UQ3
- Type
- protein
- Length
- 760 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…
- UniProt
- P01892, P61769
- Ligands
- XY1
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 28% helix, 40% strand | P01892 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E, F | Azobenzene-containing peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- XY1 · 4-[(E)-[5-(2-azanylethyl)-2-oxidanyl-phenyl] diazenyl]benzoic acid · ligand · 2 copies · chains A, E, C, F
- IPA · Isopropyl alcohol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.79 | 0.81 | 84 | IPA |
| 2 | 734 | 0.71 | 0.78 | 59 | empty |
| 3 | 180 | 0.53 | 0.79 | 32 | empty |
| 4 | 147 | 0.51 | 0.79 | 33 | empty |
| 5 | 155 | 0.49 | 0.78 | 32 | IPA |
Interfaces
6 interfaces between chains.
- C–D · 1415 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1365 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 954 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 587 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 582 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent, 2 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 4UQ3 · Crystal structure of HLA-A0201 in complex with an azobenzene- containing peptide · the same entry in another collection · chain F against F, 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4UQ3 · PDBe 4UQ3 · UniProt P01892 · UniProt P61769
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