MolNFT v1 · #148669 · protein
Crystal structure of the PDE4D catalytic domain in complex with gebr- 32A
6FDC: “Crystal structure of the PDE4D catalytic domain in complex with gebr- 32A”. X-ray diffraction, 4 ligands (DD5, D5N, MG). MolNFT v1 #148669 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FDC
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q08499
- Ligands
- DD5, D5N, MG, ZN
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 329 | — | Q08499 |
| B | — | protein | 324 | — | Q08499 |
Ligands and binding sites
- DD5 · (2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol · ligand · chains A
- D5N · (2~{S})-1-[5-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol · ligand · chains B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6FDC · Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a · 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 6FDC · PDBe 6FDC · UniProt Q08499
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