Research workbench

Human phosphdiesterase 9 substrate complex (es complex)

Analyse Human phosphdiesterase 9 substrate complex (es complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DYL
Type: protein
Length: 656 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human phosphodiesterase 9
EC: 3.1.4.35
UniProt: O76083
Ligands: PCG, IBM, MN, MG
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Human phosphodiesterase 9 (EC 3.1.4.35)	protein	328	71% helix, 0% strand	O76083

Ligands and binding sites

PCG · Cyclic guanosine monophosphate · ligand · chains A
IBM · 3-isobutyl-1-methylxanthine · ligand · chains B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
FMT · Formic acid · additive · chains B

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	377	0.73	0.84	48	MG, PCG
2	340	0.72	0.84	40	MG, IBM, FMT
3	72	0.42	0.81	16	empty
4	108	0.38	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 882 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3DYL · human phosphdiesterase 9 substrate complex (ES complex) · the same entry in another collection · chain A against A, TM-score 1.00
O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O76083
Elsewhere: RCSB PDB 3DYL · PDBe 3DYL · UniProt O76083

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