MolNFT v1 · #11515 · protein
Structure of E.COLI undecaprenyl pyrophosphate synthase
1JP3: “Structure of E.COLI undecaprenyl pyrophosphate synthase”. X-ray diffraction, 1 ligand (EGC), 5 pockets (best druggability 0.72). MolNFT v1 #11515 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JP3
- Type
- protein
- Length
- 425 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
- P60472
- Ligands
- EGC
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 214 | 49% helix, 14% strand | P60472 |
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 211 | 50% helix, 14% strand | P60472 |
Ligands and binding sites
- EGC · 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-tetramethyl-butyl)-phenoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.72 | 0.83 | 42 | EGC |
| 2 | 657 | 0.72 | 0.79 | 47 | empty |
| 3 | 56 | 0.38 | 0.81 | 16 | empty |
| 4 | 58 | 0.37 | 0.80 | 21 | empty |
| 5 | 71 | 0.29 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1847 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1JP3 · Structure of E.coli undecaprenyl pyrophosphate synthase · the same entry in another collection · chain B against B, 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 0.96
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 1JP3 · PDBe 1JP3 · UniProt P60472
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