Research workbench
Crystal structure of the apo form of the catalytic domain of PDE4D2
Analyse Crystal structure of the apo form of the catalytic domain of PDE4D2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SL3
- Type
- protein
- Length
- 1,295 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
- ZN, PO4
- Pockets
- 15 · 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 | 327 | 66% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 320 | 67% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 324 | 67% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 324 | 68% helix, 1% strand | Q08499 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 60 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, D, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.86 | 0.90 | 79 | EDO |
| 2 | 440 | 0.72 | 0.82 | 41 | ZN, PO4, EDO |
| 3 | 143 | 0.72 | 0.91 | 19 | EDO |
| 4 | 447 | 0.72 | 0.82 | 39 | EDO, ZN, PO4, DMS |
| 5 | 453 | 0.71 | 0.81 | 44 | EDO, ZN, PO4 |
Interfaces
6 interfaces between chains.
- A–C · 922 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 909 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 708 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 689 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 236 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3SL3 · Crystal structure of the apo form of the catalytic domain of PDE4D2 · 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 3SL3 · PDBe 3SL3 · UniProt Q08499
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