Research workbench
Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-1354
Analyse Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-1354 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H2J
- Type
- protein
- Length
- 428 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
- 0YU
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 217 | 46% helix, 14% strand | P60472 |
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 211 | 47% helix, 14% strand | P60472 |
Ligands and binding sites
- 0YU · N~4~-[4-(4,5-dihydro-1H-imidazol-2-yl)phenyl]-N~1~-[4-(1H-imidazol-2-yl)phenyl]-2-nitrobenzene-1,4-dicarboxamide · ligand · 2 copies · chains A, B
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 | 236 | 0.62 | 0.81 | 29 | 0YU |
| 2 | 251 | 0.61 | 0.80 | 32 | 0YU |
| 3 | 62 | 0.40 | 0.80 | 16 | empty |
| 4 | 55 | 0.35 | 0.79 | 16 | empty |
| 5 | 62 | 0.27 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1852 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4H2J · Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1354 · 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 4H2J · PDBe 4H2J · UniProt P60472
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