Research workbench
Crystal structure of E. COLI undecaprenyl pyrophosphate synthase in complex with clomiphene
Analyse Crystal structure of E. COLI undecaprenyl pyrophosphate synthase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CQJ
- Type
- protein
- Length
- 418 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
- 53Q
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 47% 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 | 212 | 48% helix, 13% strand | P60472 |
| B | DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)- farnesyl-diphosphate specific) (EC 2.5.1.31) | protein | 206 | 47% helix, 15% strand | P60472 |
Ligands and binding sites
- 53Q · Clomifene · 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 | 321 | 0.64 | 0.80 | 37 | 53Q |
| 2 | 348 | 0.63 | 0.79 | 36 | empty |
| 3 | 61 | 0.34 | 0.78 | 18 | empty |
| 4 | 92 | 0.33 | 0.73 | 19 | empty |
| 5 | 56 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1867 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5CQJ · Crystal structure of E. coli undecaprenyl pyrophosphate synthase in complex with… · 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 0.98
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 5CQJ · PDBe 5CQJ · UniProt P60472
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