Research workbench
Crystal structure of a probable undecaprenyl diphosphate synthase (upps) from campylobacter jejuni
Analyse Crystal structure of a probable undecaprenyl diphosphate synthase (upps) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UGS
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthase
- EC
- 2.5.1.31
- UniProt
- Q9PP99
- Ligands
- FFT
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 208 | 43% helix, 19% strand | Q9PP99 |
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 205 | 45% helix, 18% strand | Q9PP99 |
Ligands and binding sites
- FFT · (2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl dihydrogen phosphate · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.76 | 0.81 | 51 | FFT |
| 2 | 681 | 0.75 | 0.80 | 57 | FFT |
Interfaces
1 interface between chains.
- B–A · 1803 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3UGS · Crystal structure of a probable undecaprenyl diphosphate synthase (uppS) from… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9PP99 · AlphaFold monomer V2.0 prediction for isoprenyl transferase (Q9PP99) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9PP99
- Elsewhere: RCSB PDB 3UGS · PDBe 3UGS · UniProt Q9PP99
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