MolNFT v1 · #158084 · protein
Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with BPN14770
6NJJ · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with BPN14770”. X-ray diffraction, 4 ligands (KR7, ZN, MG), 10 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 6NJJ
- Type
- protein
- Length
- 1,339 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- KR7, ZN, MG, SO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 334 | 68% helix, 0% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 337 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- KR7 · (4-{[2-(3-chlorophenyl)-6-(trifluoromethyl)pyridin-4-yl]methyl}phenyl)acetic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.82 | 0.84 | 101 | MG, KR7 |
| 2 | 976 | 0.82 | 0.83 | 98 | BTB, ZN |
| 3 | 475 | 0.82 | 0.89 | 58 | MG, KR7 |
| 4 | 1157 | 0.81 | 0.83 | 117 | BTB, ZN |
| 5 | 471 | 0.81 | 0.88 | 59 | MG, KR7 |
Interfaces
5 interfaces between chains.
- A–B · 804 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 799 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 749 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 724 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 214 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6NJJ · Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770 · 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 6NJJ · PDBe 6NJJ · UniProt Q08499
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