MolNFT v1 · #141731 · protein
Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-981
5ZHE · DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)…: “Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-981”. X-ray diffraction, 1 ligand (HJX), 5 pockets (best druggability 0.67). MolNFT v1 #141731…
- PDB
- 5ZHE
- Type
- protein
- Length
- 406 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
- HJX
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% 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 | 206 | 42% helix, 15% strand | P60472 |
| B | DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)- farnesyl-diphosphate specific) (EC 2.5.1.31) | protein | 200 | 46% helix, 15% strand | P60472 |
Ligands and binding sites
- HJX · 2-hydroxy-6-(tetradecyloxy)benzoic acid · ligand · chains 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 | 396 | 0.67 | 0.80 | 35 | empty |
| 2 | 318 | 0.64 | 0.80 | 32 | HJX |
| 3 | 57 | 0.38 | 0.80 | 17 | empty |
| 4 | 95 | 0.34 | 0.73 | 24 | empty |
| 5 | 53 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1765 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5ZHE · Structure of E. COLI undecaprenyl diphosphate synthase in complex with bph-981 · 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 0.97
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 5ZHE · PDBe 5ZHE · UniProt P60472
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.