MolNFT v1 · #60014 · protein

Structure of EPAC2 in complex with cyclic-AMP and rap

3CF6 · Rap guanine nucleotide exchange factor (gef) 4: “Structure of EPAC2 in complex with cyclic-AMP and rap”. X-ray diffraction, 2 ligands (SP1, SO4), 11 pockets (best druggability 0.77). MolNFT v1 #60014 on GenesisL1: 3D structure…

PDB: 3CF6
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 (gef) 4; RAS-related protein rap-1B
UniProt: A2ASW3, P61224
Ligands: SP1, SO4
Pockets: 11 · 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 (gef) 4	protein	627	54% helix, 16% strand	A2ASW3
R	RAS-related protein rap-1B	protein	150	34% helix, 22% strand	P61224

Ligands and binding sites

SP1 · 6-(6-amino-purin-9-yl)-2-thioxo-tetrahydro-2-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol · ligand · 2 copies · chains E
SO4 · Sulfate ion · ion · chains R

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

Pockets

11 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	1170	0.77	0.79	89	SO4
2	309	0.76	0.88	42	SP1
3	168	0.60	0.83	34	empty
4	217	0.57	0.79	36	empty
5	142	0.49	0.78	22	empty

Interfaces

1 interface between chains.

E–R · 1652 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3CF6 · Structure of Epac2 in complex with cyclic-AMP and Rap · 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

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 A2ASW3
Every structure of UniProt P61224
Elsewhere: RCSB PDB 3CF6 · PDBe 3CF6 · UniProt A2ASW3 · UniProt P61224

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