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Crystal structure of cyclic gmp-AMP specifc phosphodiesterases in V.CHOLERAE (V-CGAP3)

Analyse Crystal structure of cyclic gmp-AMP specifc phosphodiesterases in V.CHOLERAE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z7C
Type: protein
Length: 414 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3'3'-cgamp-specific phosphodiesterase 3
EC: 3.1.4.-
UniProt: Q9KL18
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 61% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3'3'-cgamp-specific phosphodiesterase 3 (EC 3.1.4.-)	protein	414	61% helix, 2% strand	Q9KL18

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	653	0.77	0.83	85	empty
2	136	0.46	0.77	24	empty
3	147	0.42	0.75	21	empty
4	131	0.41	0.75	19	empty
5	133	0.40	0.74	22	empty

Compared structures

5Z7C · crystal structure of cyclic GMP-AMP specifc phosphodiesterases in V.cholerae (V-cGAP3) · the same entry in another collection · chain A against A, TM-score 1.00
Q9KL18 · AlphaFold monomer V2.0 prediction for 3'3'-cgamp-specific phosphodiesterase 3 (Q9KL18) · a predicted model of the same protein · chain A against A, TM-score 0.74

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 Q9KL18
Elsewhere: RCSB PDB 5Z7C · PDBe 5Z7C · UniProt Q9KL18

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