Research workbench
Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with T-49
Analyse Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NJI
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- 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
- KR4, ZN, MG
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 339 | 68% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 335 | 69% helix, 1% strand | Q08499 |
Ligands and binding sites
- KR4 · 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.84 | 0.93 | 50 | MG, KR4 |
| 2 | 353 | 0.82 | 0.91 | 52 | MG, KR4 |
| 3 | 518 | 0.68 | 0.78 | 45 | empty |
| 4 | 521 | 0.67 | 0.78 | 41 | empty |
| 5 | 150 | 0.62 | 0.85 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 308 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6NJI · Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49 · 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 6NJI · PDBe 6NJI · UniProt Q08499
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