MolNFT v1 · #141633 · protein
Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with bph-981
5ZE6 · Octaprenyl diphosphate synthase: “Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with bph-981”. X-ray diffraction, 2 ligands (HJX, MG), 10 pockets (best druggability 0.82). MolNFT v1 #141633 on…
- PDB
- 5ZE6
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Octaprenyl diphosphate synthase
- EC
- 2.5.1.90
- UniProt
- P0AD57
- Ligands
- HJX, MG
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Octaprenyl diphosphate synthase (EC 2.5.1.90) | protein | 315 | 76% helix, 1% strand | P0AD57 |
| B | Octaprenyl diphosphate synthase (EC 2.5.1.90) | protein | 313 | 77% helix, 1% strand | P0AD57 |
| C | Octaprenyl diphosphate synthase (EC 2.5.1.90) | protein | 297 | 76% helix, 0% strand | P0AD57 |
| D | Octaprenyl diphosphate synthase (EC 2.5.1.90) | protein | 307 | 79% helix, 0% strand | P0AD57 |
Ligands and binding sites
- HJX · 2-hydroxy-6-(tetradecyloxy)benzoic acid · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.82 | 0.83 | 105 | HJX, MG |
| 2 | 1004 | 0.82 | 0.83 | 79 | HJX |
| 3 | 467 | 0.71 | 0.81 | 57 | empty |
| 4 | 449 | 0.63 | 0.77 | 40 | empty |
| 5 | 188 | 0.56 | 0.79 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1879 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1811 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 351 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZE6 · Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with bph-981 · the same entry in another collection · chain D against D, TM-score 1.00
- P0AD57 · AlphaFold monomer V2.0 prediction for octaprenyl diphosphate synthase (P0AD57) · 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 P0AD57
- Elsewhere: RCSB PDB 5ZE6 · PDBe 5ZE6 · UniProt P0AD57
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