Research workbench

Complex of ARL2 and pde delta, crystal form 2 (native)

Analyse Complex of ARL2 and pde delta, crystal form 2 (native) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KSH
Type: protein
Length: 307 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, MG, PO4
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arf-like protein 2	protein	165	35% helix, 25% strand	Q9D0J4
B	Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase delta-subunit (EC 3.1.4.17)	protein	142	11% helix, 59% strand	O43924

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
PO4 · Phosphate ion · ion · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	149	0.52	0.80	29	empty
2	136	0.51	0.79	19	empty
3	102	0.44	0.78	23	MG, PO4, GDP
4	74	0.33	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 863 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (artifact).

Compared structures

1KSH · Complex of Arl2 and PDE delta, Crystal Form 2 (native) · 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 1KSH · PDBe 1KSH · UniProt Q9D0J4 · UniProt O43924

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