MolNFT v1 · #107885 · protein
Crystal structure of HLA-A1101 in complex with an azobenzene-containing peptide
4UQ2 · HLA class I histocompatibility antigen, a-11 alpha chain: “Crystal structure of HLA-A1101 in complex with an azobenzene-containing peptide”. X-ray diffraction, 1 ligand (XY1), 12 pockets (best druggability 0.81). MolNFT v1 #107885…
- PDB
- 4UQ2
- 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-11 alpha chain; Beta-2-microglobulin…
- UniProt
- P13746, P61769
- Ligands
- XY1
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen, a-11 alpha chain | protein | 275 | 27% helix, 40% strand | P13746 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| E, G | Azobenzene-containing peptide | protein | 6 | 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, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.81 | 0.82 | 86 | XY1 |
| 2 | 563 | 0.67 | 0.77 | 53 | empty |
| 3 | 548 | 0.67 | 0.78 | 60 | empty |
| 4 | 189 | 0.50 | 0.77 | 35 | empty |
| 5 | 175 | 0.48 | 0.77 | 29 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1406 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1388 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 501 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 417 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 413 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 4UQ2 · Crystal structure of HLA-A1101 in complex with an azobenzene- containing peptide · the same entry in another collection · chain G against G, 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 P13746
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4UQ2 · PDBe 4UQ2 · UniProt P13746 · UniProt P61769
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