Research workbench
Complex of ARL2 and pde delta, crystal form 1
Analyse Complex of ARL2 and pde delta, crystal form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KSG
- Type
- protein
- Length
- 308 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
- GTP, MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arf-like protein 2 | protein | 180 | 37% helix, 23% strand | Q9D0J4 |
| B | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase delta-subunit (EC 3.1.4.17) | protein | 128 | 11% helix, 52% strand | O43924 |
Ligands and binding sites
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 | 286 | 0.66 | 0.81 | 29 | empty |
| 2 | 136 | 0.55 | 0.82 | 25 | empty |
| 3 | 121 | 0.46 | 0.78 | 24 | MG, GTP |
| 4 | 96 | 0.36 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 912 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1KSG · Complex of Arl2 and PDE delta, Crystal Form 1 · 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 0.91
- 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 0.82
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 Q9D0J4
- Every structure of UniProt O43924
- Elsewhere: RCSB PDB 1KSG · PDBe 1KSG · UniProt Q9D0J4 · UniProt O43924
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