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Catalytic domain of human phosphodiesterase 3B in complex with ibmx
Analyse Catalytic domain of human phosphodiesterase 3B in complex with ibmx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SOJ
- Type
- protein
- Length
- 4,470 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-inhibited 3',5'-cyclic phosphodiesterase B
- EC
- 3.1.4.17
- UniProt
- Q13370
- Ligands
- IBM, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Cgmp-inhibited 3',5'-cyclic phosphodiesterase B (EC 3.1.4.17) | protein | 364 | 62% helix, 1% strand | Q13370 |
| B, D, F, H, J, L | Cgmp-inhibited 3',5'-cyclic phosphodiesterase B (EC 3.1.4.17) | protein | 381 | 60% helix, 2% strand | Q13370 |
Ligands and binding sites
- IBM · 3-isobutyl-1-methylxanthine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.77 | 0.79 | 83 | empty |
| 2 | 912 | 0.75 | 0.79 | 84 | empty |
| 3 | 901 | 0.75 | 0.79 | 69 | empty |
| 4 | 446 | 0.72 | 0.82 | 48 | MG, IBM |
| 5 | 428 | 0.72 | 0.82 | 44 | MG, IBM |
Interfaces
24 interfaces between chains.
- E–F · 914 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 913 Ų buried · 16 hydrogen bonds · protein-protein
- A–J · 910 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 906 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 904 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1SOJ · Catalytic domain of human phosphodiesterase 3B in complex with ibmx · the same entry in another collection · chain L against L, 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 Q13370
- Elsewhere: RCSB PDB 1SOJ · PDBe 1SOJ · UniProt Q13370
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