Research workbench
Crystal structure of phosphodiesterase domain of rhopde fusion protein from the choanoflagellate salpingoeca rosetta
Analyse Crystal structure of phosphodiesterase domain of rhopde fusion protein from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VYD
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- F2TZN0
- Ligands
- ZN, MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase (EC 3.1.4.-) | protein | 314 | 72% helix, 0% strand | F2TZN0 |
| B | Phosphodiesterase (EC 3.1.4.-) | protein | 317 | 71% helix, 0% strand | F2TZN0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.73 | 0.83 | 44 | MG |
| 2 | 405 | 0.71 | 0.82 | 41 | MG |
| 3 | 196 | 0.47 | 0.75 | 18 | empty |
| 4 | 64 | 0.40 | 0.80 | 15 | empty |
| 5 | 150 | 0.40 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 859 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5VYD · Crystal structure of phosphodiesterase domain of RhoPDE fusion protein from the… · 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 F2TZN0
- Elsewhere: RCSB PDB 5VYD · PDBe 5VYD · UniProt F2TZN0
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