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Crystal structure of yeast CAPDE2 in complex with ibmx

Analyse Crystal structure of yeast CAPDE2 in complex with ibmx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CPT
Type: protein
Length: 519 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphodiesterase
EC: 3.1.4.-
UniProt: Q8NJP9
Ligands: IBM, ZN, MG
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 60% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphodiesterase (EC 3.1.4.-)	protein	519	60% helix, 5% strand	Q8NJP9

Ligands and binding sites

IBM · 3-isobutyl-1-methylxanthine · ligand · chains A
ZN · Zinc ion · metal · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	375	0.68	0.81	40	MG, IBM
2	185	0.60	0.82	28	empty
3	85	0.41	0.78	12	empty
4	50	0.26	0.74	12	empty

Compared structures

6CPT · crystal structure of yeast caPDE2 in complex with IBMX · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8NJP9
Elsewhere: RCSB PDB 6CPT · PDBe 6CPT · UniProt Q8NJP9

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