Research workbench

Rhogap domain of ARAP3 in complex with rhoa in the transition state

Analyse Rhogap domain of ARAP3 in complex with rhoa in the transition state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JCP
Type: protein
Length: 720 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arf-gap with rho-gap domain, ank repeat and pH domain- containing protein…
UniProt: Q8WWN8, P61586
Ligands: GDP, ALF, MG
Pockets: 6 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Arf-gap with rho-gap domain, ank repeat and pH domain- containing protein 3,LINKER,TRANSFORMING protein rhoa	protein	359	56% helix, 12% strand	Q8WWN8, P61586
A	Arf-gap with rho-gap domain, ank repeat and pH domain- containing protein 3,LINKER,TRANSFORMING protein rhoa	protein	361	56% helix, 12% strand	Q8WWN8, P61586

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, A
ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains B, A
MG · Magnesium ion · metal · 2 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	627	0.71	0.79	89	GDP, MG, ALF
2	679	0.71	0.78	87	GDP, MG, ALF
3	96	0.70	0.93	21	empty
4	88	0.69	0.93	20	empty
5	103	0.33	0.72	17	empty

Interfaces

1 interface between chains.

B–A · 738 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5JCP · RhoGAP domain of ARAP3 in complex with RhoA in the transition state · the same entry in another collection · chain B against B, TM-score 1.00
Q8WWN8 · AlphaFold monomer V2.0 prediction for arf-gap with rho-gap domain, ank repeat and pH… · a predicted model of the same protein · chain A against A, TM-score 0.55
P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain B against A, TM-score 0.46

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 Q8WWN8
Every structure of UniProt P61586
Elsewhere: RCSB PDB 5JCP · PDBe 5JCP · UniProt Q8WWN8 · UniProt P61586

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