MolNFT v1 · #74507 · protein
Crystal structure of polyprenyl synthase from caulobacter crescentus CB15 complexed with calcium and isoprenyl diphosphate
3OYR · Trans-isoprenyl diphosphate synthase: “Crystal structure of polyprenyl synthase from caulobacter crescentus CB15 complexed with calcium and…”. X-ray diffraction, 3 ligands (DMA, POP, CA), 5 pockets (best druggability 0.81). MolNFT…
- 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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