Research workbench
Complex of ARL2 and pde delta, crystal form 2 (semet)
Analyse Complex of ARL2 and pde delta, crystal form 2 (semet) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KSJ
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arf-like protein 2; Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase…
- EC
- 3.1.4.17
- UniProt
- Q9D0J4, O43924
- Ligands
- GDP, GTP, MG, PO4
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arf-like protein 2 | protein | 165 | 28% helix, 27% strand | Q9D0J4 |
| B | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase delta-subunit (EC 3.1.4.17) | protein | 141 | 11% helix, 60% strand | O43924 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.53 | 0.80 | 28 | empty |
| 2 | 112 | 0.50 | 0.80 | 19 | empty |
| 3 | 110 | 0.44 | 0.78 | 24 | PO4, MG, GDP, GTP |
| 4 | 51 | 0.30 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 878 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered, artifact).
Compared structures
- 1KSJ · Complex of Arl2 and PDE delta, Crystal Form 2 (SeMet) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9D0J4 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 2 (Q9D0J4) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.84
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 Q9D0J4
- Every structure of UniProt O43924
- Elsewhere: RCSB PDB 1KSJ · PDBe 1KSJ · UniProt Q9D0J4 · UniProt O43924
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