Research workbench
Crystal structure of polyprenyl synthase from caulobacter crescentus CB15 complexed with calcium and isoprenyl diphosphate
Analyse Crystal structure of polyprenyl synthase from caulobacter crescentus CB15… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OYR
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-isoprenyl diphosphate synthase
- UniProt
- Q9A6I1
- Ligands
- DMA, POP, CA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trans-isoprenyl diphosphate synthase | protein | 292 | 73% helix, 0% strand | Q9A6I1 |
| B | Trans-isoprenyl diphosphate synthase | protein | 328 | 75% helix, 1% strand | Q9A6I1 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 2 copies · chains B
- POP · Pyrophosphate 2- · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.81 | 0.92 | 38 | DMA, CA |
| 2 | 54 | 0.70 | 0.97 | 18 | empty |
| 3 | 239 | 0.55 | 0.77 | 37 | POP |
| 4 | 142 | 0.45 | 0.76 | 24 | empty |
| 5 | 111 | 0.36 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1887 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3OYR · Crystal structure of polyprenyl synthase from Caulobacter crescentus CB15 complexed with… · 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 Q9A6I1
- Elsewhere: RCSB PDB 3OYR · PDBe 3OYR · UniProt Q9A6I1
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