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Crystal structure of human phosphodiesterase 4D with D155988/PMNPQ
Analyse Crystal structure of human phosphodiesterase 4D with D155988/PMNPQ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G58
- Type
- protein
- Length
- 1,334 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
- 988, ZN, MG, SO4
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 335 | 65% helix, 1% strand | Q08499 |
| B, C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 327 | 67% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 345 | 64% helix, 1% strand | Q08499 |
Ligands and binding sites
- 988 · 8-(3-nitrophenyl)-6-(pyridin-4-ylmethyl)quinoline · 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 · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, C, B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.88 | 0.89 | 151 | EDO |
| 2 | 402 | 0.82 | 0.90 | 52 | MG, 988, EDO |
| 3 | 656 | 0.79 | 0.84 | 65 | EDO |
| 4 | 471 | 0.71 | 0.81 | 46 | MG, 988, EDO |
| 5 | 480 | 0.71 | 0.81 | 46 | MG, 988 |
Interfaces
6 interfaces between chains.
- B–D · 949 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 908 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 859 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 843 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 273 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3G58 · Crystal structure of human phosphodiesterase 4d with d155988/pmnpq · 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 3G58 · PDBe 3G58 · UniProt Q08499
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