MolNFT v1 · #26798 · protein
Crystal structure of D26A mutant upps in complex with mg, ipp and fspp
1X08 · Undecaprenyl pyrophosphate synthetase: “Crystal structure of D26A mutant upps in complex with mg, ipp and fspp”. X-ray diffraction, 2 ligands (FPS, IPE), 3 pockets (best druggability 0.80). MolNFT v1 #26798 on GenesisL1: 3D…
- PDB
- 1X08
- Type
- protein
- Length
- 228 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthetase
- EC
- 2.5.1.31
- UniProt
- P60472
- Ligands
- FPS, IPE
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 228 | 50% helix, 15% strand | P60472 |
Ligands and binding sites
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · 2 copies · chains A
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.80 | 0.87 | 59 | FPS, IPE |
| 2 | 92 | 0.34 | 0.74 | 18 | empty |
| 3 | 55 | 0.33 | 0.78 | 16 | empty |
Compared structures
- 1X08 · Crystal structure of D26A mutant UPPs in complex with Mg, IPP and FsPP · the same entry in another collection · chain A against A, TM-score 1.00
- P60472 · AlphaFold monomer V2.0 prediction for DITRANS,POLYCIS-undecaprenyl- diphosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P60472
- Elsewhere: RCSB PDB 1X08 · PDBe 1X08 · UniProt P60472
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