Research workbench
Crystal structure of the complex of the PDZ tandem of syntenin with an interleukin 5 receptor alpha peptide.
Analyse Crystal structure of the complex of the PDZ tandem of syntenin with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OBZ
- Type
- protein
- Length
- 332 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntenin 1; Interleukin 5 receptor alpha
- UniProt
- O00560, Q01344
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syntenin 1 | protein | 163 | 17% helix, 39% strand | O00560 |
| B | Syntenin 1 | protein | 165 | 16% helix, 38% strand | O00560 |
| P | Interleukin 5 receptor alpha | protein | 4 | 0% helix, 0% strand | Q01344 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.52 | 0.80 | 22 | empty |
| 2 | 72 | 0.35 | 0.76 | 14 | ACT |
Interfaces
2 interfaces between chains.
- A–B · 1233 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 374 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1OBZ · Crystal structure of the complex of the PDZ tandem of syntenin with an interleukin 5… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01344 · AlphaFold monomer V2.0 prediction for interleukin-5 receptor subunit alpha (Q01344) · a predicted model of the same protein · chain P against A, TM-score 0.82
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 O00560
- Every structure of UniProt Q01344
- Elsewhere: RCSB PDB 1OBZ · PDBe 1OBZ · UniProt O00560 · UniProt Q01344
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