MolNFT v1 · #123197 · protein

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

5JCP · Arf-gap with rho-gap domain, ank repeat and pH domain…: “Rhogap domain of ARAP3 in complex with rhoa in the transition state”. X-ray diffraction, 3 ligands (GDP, ALF, MG), 6 pockets (best druggability 0.71). MolNFT v1 #123197 on…

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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