MolNFT v1 · #20631 · protein

Crystal structure of PDE5A1-ibmx

1RKP · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Crystal structure of PDE5A1-ibmx”. X-ray diffraction, 3 ligands (IBM, ZN, MG), 3 pockets (best druggability 0.63). MolNFT v1 #20631 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1RKP
Type: protein
Length: 311 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cgmp-specific 3',5'-cyclic phosphodiesterase
EC: 3.1.4.17
UniProt: O76074
Ligands: IBM, ZN, MG
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	311	69% helix, 0% strand	O76074

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

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	320	0.63	0.80	35	MG, IBM
2	114	0.51	0.81	27	empty
3	80	0.45	0.81	23	empty

Compared structures

1RKP · Crystal structure of PDE5A1-IBMX · the same entry in another collection · chain A against A, TM-score 1.00
O76074 · AlphaFold monomer V2.0 prediction for cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 O76074
Elsewhere: RCSB PDB 1RKP · PDBe 1RKP · UniProt O76074

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