Research workbench
HPDE2A catalytic domain complexed with ibmx
Analyse HPDE2A catalytic domain complexed with ibmx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ITU
- Type
- protein
- Length
- 1,325 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
- IBM, ZN, MG
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 338 | 69% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 333 | 70% helix, 0% strand | O00408 |
| C, D | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 327 | 69% helix, 0% strand | O00408 |
Ligands and binding sites
- IBM · 3-isobutyl-1-methylxanthine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium 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
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.83 | 0.84 | 106 | MG, IBM |
| 2 | 388 | 0.73 | 0.84 | 43 | MG, IBM |
| 3 | 828 | 0.73 | 0.78 | 70 | empty |
| 4 | 358 | 0.72 | 0.84 | 38 | MG, IBM |
| 5 | 375 | 0.72 | 0.83 | 37 | MG, IBM |
Interfaces
5 interfaces between chains.
- C–D · 884 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 786 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 764 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 379 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 3ITU · PDBe 3ITU · UniProt O00408
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