Research workbench
Structure of a phosphatidylinositolphosphate (pip) synthase from renibacterium salmoninarum
Analyse Structure of a phosphatidylinositolphosphate (pip) synthase from renibacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D92
- Type
- protein
- Length
- 1,358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AF2299 PROTEIN,PHOSPHATIDYLINOSITOL synthase
- UniProt
- O27985, A9WSF5
- Ligands
- 8K6, 58A, MG
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | AF2299 PROTEIN,PHOSPHATIDYLINOSITOL synthase | protein | 342 | 61% helix, 12% strand | O27985, A9WSF5 |
| A | AF2299 PROTEIN,PHOSPHATIDYLINOSITOL synthase | protein | 340 | 61% helix, 12% strand | O27985, A9WSF5 |
| C | AF2299 PROTEIN,PHOSPHATIDYLINOSITOL synthase | protein | 334 | 60% helix, 12% strand | O27985, A9WSF5 |
Ligands and binding sites
- 8K6 · Octadecane · ligand · 33 copies · chains D, A, B, C
- 58A · 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9e)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy) phosphoryl]cytidine · ligand · 4 copies · chains D, A, B, C
- MG · Magnesium ion · metal · 8 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.66 | 0.77 | 54 | MG, 58A |
| 2 | 550 | 0.66 | 0.77 | 62 | 58A |
| 3 | 445 | 0.62 | 0.76 | 60 | MG, 58A |
| 4 | 222 | 0.56 | 0.79 | 27 | empty |
| 5 | 58 | 0.55 | 0.88 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1828 Ų buried · 9 hydrogen bonds · protein-protein
- D–A · 1770 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 455 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
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 O27985
- Every structure of UniProt A9WSF5
- Elsewhere: RCSB PDB 5D92 · PDBe 5D92 · UniProt O27985 · UniProt A9WSF5
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