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Crystal structure of human phosphodiesterase 12

Analyse Crystal structure of human phosphodiesterase 12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZKF
Type: protein
Length: 462 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2',5'-phosphodiesterase 12
EC: 3.1.4.-, 3.1.13.4
UniProt: Q6L8Q7
Ligands: MG
Pockets: 3 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2',5'-phosphodiesterase 12 (EC 3.1.4.-, 3.1.13.4)	protein	462	27% helix, 29% strand	Q6L8Q7

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A

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

Pockets

3 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	337	0.58	0.76	41	MG
2	121	0.51	0.81	17	empty
3	103	0.45	0.79	17	empty

Compared structures

4ZKF · Crystal structure of human phosphodiesterase 12 · the same entry in another collection · chain A against A, TM-score 1.00
Q6L8Q7 · AlphaFold monomer V2.0 prediction for 2',5'-phosphodiesterase 12 (Q6L8Q7) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q6L8Q7
Elsewhere: RCSB PDB 4ZKF · PDBe 4ZKF · UniProt Q6L8Q7

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