MolNFT v1 · #158082 · protein
Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with T-48
6NJH · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with T-48”. X-ray diffraction, 3 ligands (KRD, MG, ZN), 17 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6NJH
- Type
- protein
- Length
- 1,339 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- KRD, MG, ZN
- Pockets
- 17 · best druggability 0.83
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 3.1.4.53) | protein | 334 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 335 | 67% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 337 | 67% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 333 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- KRD · 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)acetamide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D
- ZN · Zinc 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
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.83 | 0.92 | 48 | MG, KRD |
| 2 | 725 | 0.80 | 0.84 | 96 | MG, KRD |
| 3 | 482 | 0.80 | 0.87 | 69 | MG, KRD |
| 4 | 478 | 0.80 | 0.87 | 65 | MG, KRD |
| 5 | 352 | 0.76 | 0.86 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–C · 802 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 763 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 727 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 710 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NJH · Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48 · 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 6NJH · PDBe 6NJH · UniProt Q08499
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