MolNFT v1 · #148510 · protein
Crystal structure of the PDE4D catalytic domain in complex with gebr- 4A
6F8T · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the PDE4D catalytic domain in complex with gebr- 4A”. X-ray diffraction, 3 ligands (CZT, MG, ZN), 3 pockets (best druggability 0.72). MolNFT v1 #148510 on…
- PDB
- 6F8T
- Type
- protein
- Length
- 652 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
- CZT, MG, ZN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 65% 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 | 328 | 65% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 65% helix, 1% strand | Q08499 |
Ligands and binding sites
- CZT · (2~{R})-1-[(~{E})-(3-cyclopentyloxy-4-methoxy-phenyl) methylideneamino]oxy-3-[(2~{R},6~{S})-2,6-dimethylmorpholin-4-yl]propan-2-ol · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.72 | 0.82 | 44 | MG, CZT |
| 2 | 602 | 0.71 | 0.79 | 61 | empty |
| 3 | 436 | 0.71 | 0.81 | 41 | MG, CZT |
Interfaces
1 interface between chains.
- A–B · 786 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6F8T · Crystal structure of the PDE4D catalytic domain in complex with GEBR-4a · 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 6F8T · PDBe 6F8T · UniProt Q08499
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