MolNFT v1 · #29829 · protein
Structure of PDE4D2-ibmx
1ZKN · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Structure of PDE4D2-ibmx”. X-ray diffraction, 3 ligands (IBM, ZN, MG), 18 pockets (best druggability 0.74). MolNFT v1 #29829 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1ZKN
- Type
- protein
- Length
- 1,325 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- IBM, ZN, MG
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 334 | 66% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 327 | 66% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 330 | 67% helix, 1% strand | Q08499 |
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
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.74 | 0.93 | 20 | empty |
| 2 | 144 | 0.72 | 0.91 | 20 | empty |
| 3 | 411 | 0.72 | 0.83 | 42 | MG, IBM |
| 4 | 440 | 0.72 | 0.82 | 41 | MG, IBM |
| 5 | 447 | 0.71 | 0.82 | 40 | MG, IBM |
Interfaces
6 interfaces between chains.
- B–D · 1006 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 912 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 911 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 874 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 248 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1ZKN · Structure of PDE4D2-IBMX · the same entry in another collection · chain A against A, 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 Q08499
- Elsewhere: RCSB PDB 1ZKN · PDBe 1ZKN · UniProt Q08499
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