Research workbench
Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-789
Analyse Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-789 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WYJ
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)- farnesyl-diphosphate specific)
- EC
- 2.5.1.31
- UniProt
- P60472
- Ligands
- H78
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)- farnesyl-diphosphate specific) (EC 2.5.1.31) | protein | 222 | 49% helix, 14% strand | P60472 |
| B | DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)- farnesyl-diphosphate specific) (EC 2.5.1.31) | protein | 219 | 49% helix, 14% strand | P60472 |
Ligands and binding sites
- H78 · [1-oxidanyl-2-[3-[3-[[3-[[3-[3-(2-oxidanyl-2,2-diphosphono-ethyl)phenyl]phenyl]sulfamoyl]phenyl]sulfonylamino]phenyl]phenyl]-1-phosphono-ethyl]phosphonic acid · ligand · chains A
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 | 662 | 0.71 | 0.78 | 49 | empty |
| 2 | 670 | 0.71 | 0.78 | 52 | H78 |
| 3 | 69 | 0.38 | 0.79 | 23 | empty |
| 4 | 60 | 0.38 | 0.80 | 20 | empty |
| 5 | 102 | 0.35 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1971 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3WYJ · Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789 · 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 0.94
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 3WYJ · PDBe 3WYJ · UniProt P60472
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