MolNFT v1 · #26797 · protein
Crystal structure of undecaprenyl pyrophosphate synthase in complex with mg and ipp
1X07 · Undecaprenyl pyrophosphate synthetase: “Crystal structure of undecaprenyl pyrophosphate synthase in complex with mg and ipp”. X-ray diffraction, 3 ligands (IPE, MG, PO4), 3 pockets (best druggability 0.78). MolNFT v1 #26797 on…
- PDB
- 1X07
- Type
- protein
- Length
- 231 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
- IPE, MG, PO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 231 | 48% helix, 15% strand | P60472 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 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 | 414 | 0.78 | 0.87 | 61 | PO4, MG, IPE |
| 2 | 71 | 0.36 | 0.77 | 18 | empty |
| 3 | 83 | 0.34 | 0.75 | 19 | empty |
Compared structures
- 1X07 · Crystal structure of undecaprenyl pyrophosphate synthase in complex with Mg and IPP · 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 0.98
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 1X07 · PDBe 1X07 · UniProt P60472
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