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Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, crystal form 1
Analyse Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FYO
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- PSEUDOMONAS SP.
- Molecule
- Phosphoinositol-specific phospholipase C
- Ligands
- CA
- Pockets
- 4 · best druggability 0.34
Structure
x-ray diffraction · resolution 1.5 · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoinositol-specific phospholipase C | protein | 298 | 33% helix, 18% strand | — |
| B | Phosphoinositol-specific phospholipase C | protein | 294 | 33% helix, 18% strand | — |
Ligands and binding sites
- CA · Calcium 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.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.34 | 0.76 | 19 | CA |
| 2 | 73 | 0.33 | 0.76 | 20 | empty |
| 3 | 76 | 0.29 | 0.72 | 12 | empty |
| 4 | 56 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5FYO · Calcium-dependent phosphoinositol-specific phospholipase C from a gram-negative… · 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
- Elsewhere: RCSB PDB 5FYO · PDBe 5FYO
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