Research workbench
Crystal structure of human phosphodiesterase 4D with D155871
Analyse Crystal structure of human phosphodiesterase 4D with D155871 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G4I
- Type
- protein
- Length
- 1,318 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, SO4
- Pockets
- 12 · best druggability 0.86
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 | 331 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 326 | 67% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 327 | 68% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 334 | 65% 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
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- EOH · Ethanol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.86 | 0.90 | 102 | EOH |
| 2 | 558 | 0.84 | 0.90 | 84 | empty |
| 3 | 466 | 0.74 | 0.83 | 47 | MG, D71 |
| 4 | 458 | 0.73 | 0.83 | 45 | MG, D71 |
| 5 | 508 | 0.73 | 0.82 | 52 | MG, D71 |
Interfaces
6 interfaces between chains.
- B–D · 927 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 895 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 886 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 867 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 255 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3G4I · Crystal structure of human phosphodiesterase 4d with 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 3G4I · PDBe 3G4I · UniProt Q08499
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