Research workbench

Selective activation of EPAC1 and EPAC2

Analyse Selective activation of EPAC1 and EPAC2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MGY
Type: protein
Length: 777 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rap guanine nucleotide exchange factor 4; RAS-related protein rap-1B
UniProt: Q9EQZ6, P61224
Ligands: H07, SO4
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Rap guanine nucleotide exchange factor 4	protein	627	54% helix, 16% strand	Q9EQZ6
R	RAS-related protein rap-1B	protein	150	33% helix, 21% strand	P61224

Ligands and binding sites

H07 · (2S,4aR,6R,7R,7aR)-6-{6-amino-8-[(4-chlorophenyl)sulfanyl]-9H-purin-9-yl}-7-methoxytetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-2-ol 2-oxide · ligand · chains E
SO4 · Sulfate ion · ion · chains R

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

Pockets

10 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	1074	0.77	0.79	83	SO4
2	448	0.75	0.84	59	H07
3	211	0.57	0.80	37	empty
4	89	0.54	0.85	20	empty
5	137	0.49	0.78	21	empty

Interfaces

1 interface between chains.

E–R · 1662 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4MGY · Selective activation of Epac1 and Epac2 · the same entry in another collection · chain E against E, TM-score 1.00
P61224 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1B (P61224) · a predicted model of the same protein · chain R against A, TM-score 0.88
Q9EQZ6 · AlphaFold monomer V2.0 prediction for rap guanine nucleotide exchange factor 4 (Q9EQZ6) · a predicted model of the same protein · chain E against A, TM-score 0.78

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 Q9EQZ6
Every structure of UniProt P61224
Elsewhere: RCSB PDB 4MGY · PDBe 4MGY · UniProt Q9EQZ6 · UniProt P61224

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