MolNFT v1 · #148447 · protein
Crystal structure of the PDE4D catalytic domain in complex with gebr- 7B
6F6U · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the PDE4D catalytic domain in complex with gebr- 7B”. X-ray diffraction, 3 ligands (CV8, MG, ZN), 6 pockets (best druggability 0.71). MolNFT v1 #148447 on…
- PDB
- 6F6U
- 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
- CV8, MG, ZN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 66% 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 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- CV8 · 2-[(~{E})-(3-cyclopentyloxy-4-methoxy-phenyl) methylideneamino]oxy-1-[(2~{R},6~{S})-2,6-dimethylmorpholin-4-yl]ethanone · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.71 | 0.81 | 43 | MG, CV8 |
| 2 | 416 | 0.70 | 0.81 | 43 | MG, CV8 |
| 3 | 145 | 0.54 | 0.81 | 18 | empty |
| 4 | 190 | 0.53 | 0.79 | 22 | empty |
| 5 | 99 | 0.38 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6F6U · Crystal structure of the PDE4D catalytic domain in complex with GEBR-7b · 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 6F6U · PDBe 6F6U · UniProt Q08499
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