Research workbench
Crystal structure of the D26A mutant upps in complex with magnesium and isopentenyl pyrophosphate
Analyse Crystal structure of the D26A mutant upps in complex with magnesium and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X09
- 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
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 231 | 51% helix, 15% strand | P60472 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.79 | 0.86 | 59 | MG, IPE |
| 2 | 63 | 0.28 | 0.73 | 19 | empty |
Compared structures
- 1X09 · Crystal structure of the D26A mutant UPPs in complex with magnesium and isopentenyl… · 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 0.97
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 1X09 · PDBe 1X09 · UniProt P60472
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.