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Catalytic domain of HPDE2A

Analyse Catalytic domain of HPDE2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ITM
Type: protein
Length: 1,253 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cgmp-dependent 3',5'-cyclic phosphodiesterase
EC: 3.1.4.17
UniProt: O00408
Ligands: ZN
Pockets: 19 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 68% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	307	68% helix, 1% strand	O00408
B, D	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	318	69% helix, 1% strand	O00408
C	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	310	68% helix, 1% strand	O00408

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1082	0.82	0.84	127	empty
2	351	0.79	0.89	51	empty
3	442	0.70	0.81	49	empty
4	341	0.68	0.82	33	empty
5	293	0.66	0.82	28	empty

Interfaces

6 interfaces between chains.

A–B · 1649 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1614 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 794 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 643 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 391 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3ITM · Catalytic domain of hPDE2A · the same entry in another collection · chain A against A, TM-score 1.00
O00408 · AlphaFold monomer V2.0 prediction for cgmp-dependent 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain C against A, TM-score 0.90

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 O00408
Elsewhere: RCSB PDB 3ITM · PDBe 3ITM · UniProt O00408

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