MolNFT v1 · #111776 · protein

The structure of human PDE12 residues 161-609

4Z0V · 2',5'-phosphodiesterase 12: “The structure of human PDE12 residues 161-609”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.55). MolNFT v1 #111776 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Z0V
Type: protein
Length: 434 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 0.55

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2',5'-phosphodiesterase 12 (EC 3.1.4.-, 3.1.13.4)	protein	434	27% helix, 31% strand	Q6L8Q7

Ligands and binding sites

MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · 6 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	318	0.55	0.75	35	MG, GOL
2	123	0.51	0.81	17	empty
3	150	0.48	0.77	19	GOL

Compared structures

4Z0V · The structure of human PDE12 residues 161-609 · 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 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 Q6L8Q7
Elsewhere: RCSB PDB 4Z0V · PDBe 4Z0V · UniProt Q6L8Q7

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