Research workbench
E. COLI undecaprenyl pyrophosphate synthase in complex with bph-628
Analyse E. COLI undecaprenyl pyrophosphate synthase in complex with bph-628 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E9A
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthetase
- EC
- 2.5.1.31
- UniProt
- P60472
- Ligands
- B28
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 218 | 49% helix, 14% strand | P60472 |
| B | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 214 | 51% helix, 14% strand | P60472 |
Ligands and binding sites
- B28 · (1-hydroxy-1-phosphono-2-[1,1';4',1'']terphenyl-3-yl-ethyl)-phosphonic acid · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.72 | 0.79 | 42 | B28 |
| 2 | 470 | 0.68 | 0.79 | 45 | B28 |
| 3 | 62 | 0.37 | 0.79 | 20 | empty |
| 4 | 100 | 0.35 | 0.74 | 22 | empty |
| 5 | 69 | 0.29 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1910 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2E9A · E. coli undecaprenyl pyrophosphate synthase in complex with BPH-628 · 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 B 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 2E9A · PDBe 2E9A · UniProt P60472
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