Research workbench
Crystal structure of AMPD2 phosphopeptide bound to HLA-A2
Analyse Crystal structure of AMPD2 phosphopeptide bound to HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NO3
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- 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; AMP…
- UniProt
- P01892, P61769, Q01433
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 27% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | AMP deaminase 2 | protein | 9 | 0% helix, 0% strand | Q01433 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.67 | 0.76 | 54 | EDO |
| 2 | 179 | 0.49 | 0.77 | 29 | empty |
| 3 | 66 | 0.41 | 0.80 | 15 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 1317 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 927 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 4NO3 · Crystal structure of AMPD2 phosphopeptide bound to HLA-A2 · 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
- Q01433 · AlphaFold monomer V2.0 prediction for AMP deaminase 2 (Q01433) · a predicted model of the same protein · chain C against A, TM-score 0.48
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 Q01433
- Elsewhere: RCSB PDB 4NO3 · PDBe 4NO3 · UniProt P01892 · UniProt P61769 · UniProt Q01433
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