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Crystal structure of human phosphodiesterase 4D with regulatory domain and D155871
Analyse Crystal structure of human phosphodiesterase 4D with regulatory domain and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G4G
- Type
- protein
- Length
- 1,350 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
- D71, ZN, MG, CA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 338 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 336 | 67% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 339 | 66% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 337 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- D71 · 1-(3-nitrophenyl)-3-(pyridin-4-ylmethyl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione · 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
- CA · Calcium 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.82 | 0.86 | 73 | MG, D71 |
| 2 | 695 | 0.82 | 0.86 | 77 | MG, D71 |
| 3 | 483 | 0.82 | 0.88 | 58 | MG, D71 |
| 4 | 759 | 0.80 | 0.84 | 77 | MG, D71 |
| 5 | 947 | 0.71 | 0.76 | 78 | CA |
Interfaces
3 interfaces between chains.
- A–B · 772 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 752 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 351 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3G4G · Crystal structure of human phosphodiesterase 4d with regulatory domain and d155871 · 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 3G4G · PDBe 3G4G · UniProt Q08499
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