Research workbench
Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-1248
Analyse Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-1248 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H2O
- Type
- protein
- Length
- 414 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
- 0YW
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 208 | 45% helix, 14% strand | P60472 |
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 206 | 48% helix, 14% strand | P60472 |
Ligands and binding sites
- 0YW · 2-{[3-(decyloxy)benzoyl]amino}-5-nitrobenzoic acid · ligand · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.68 | 0.81 | 41 | 0YW |
| 2 | 207 | 0.60 | 0.81 | 28 | 0YW |
| 3 | 59 | 0.52 | 0.87 | 16 | empty |
| 4 | 72 | 0.40 | 0.80 | 21 | empty |
| 5 | 61 | 0.37 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 1689 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4H2O · Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1248 · 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 4H2O · PDBe 4H2O · UniProt P60472
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