Research workbench
Crystal structure of non-phosphorylated form of PKD2 phosphopeptide bound to HLA-A2
Analyse Crystal structure of non-phosphorylated form of PKD2 phosphopeptide bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NNY
- 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…
- UniProt
- P01892, P61769, Q9BZL6
- Ligands
- CD
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 26% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | SERINE/THREONINE-protein kinase D2 | protein | 9 | 0% helix, 0% strand | Q9BZL6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.66 | 0.76 | 62 | CD |
| 2 | 57 | 0.47 | 0.84 | 18 | empty |
| 3 | 84 | 0.43 | 0.80 | 23 | empty |
| 4 | 74 | 0.40 | 0.79 | 17 | GOL |
| 5 | 68 | 0.35 | 0.77 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1330 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 868 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4NNY · Crystal structure of non-phosphorylated form of PKD2 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
- Q9BZL6 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase D2 (Q9BZL6) · 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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt Q9BZL6
- Elsewhere: RCSB PDB 4NNY · PDBe 4NNY · UniProt P01892 · UniProt P61769 · UniProt Q9BZL6
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