MolNFT v1 · #119524 · protein
Calcium-dependent phosphoinositol-specific phospholipase C from a gram-negative bacterium, pseudomonas sp, apo form, myoinositol complex
5FYR: “Calcium-dependent phosphoinositol-specific phospholipase C from a gram-negative bacterium, pseudomonas sp…”. X-ray diffraction, 3 ligands (INS, CA, PO4), 6 pockets (best druggability 0.56). MolNFT v1 #119524 on GenesisL1: 3D…
- PDB
- 5FYR
- Type
- protein
- Length
- 1,170 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoinositol-specific phospholipase C
- Ligands
- INS, CA, PO4
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoinositol-specific phospholipase C | protein | 289 | 35% helix, 19% strand | — |
| B | Phosphoinositol-specific phospholipase C | protein | 289 | 35% helix, 19% strand | — |
| C | Phosphoinositol-specific phospholipase C | protein | 295 | 34% helix, 18% strand | — |
| D | Phosphoinositol-specific phospholipase C | protein | 297 | 32% helix, 18% strand | — |
Ligands and binding sites
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.56 | 0.77 | 37 | INS |
| 2 | 160 | 0.46 | 0.76 | 20 | empty |
| 3 | 208 | 0.45 | 0.74 | 23 | empty |
| 4 | 113 | 0.40 | 0.76 | 21 | INS |
| 5 | 103 | 0.38 | 0.76 | 22 | INS |
Interfaces
2 interfaces between chains.
- A–D · 198 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 194 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5FYR · 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 5FYR · PDBe 5FYR
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