MolNFT v1 · #141859 · protein
Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with ligand bph-629
5ZLF · Octaprenyl diphosphate synthase: “Crystal structure of octaprenyl pyrophosphate synthase from escherichia COLI with ligand bph-629”. X-ray diffraction, 2 ligands (B29, MG), 16 pockets (best druggability 0.82). MolNFT v1 #141859 on…
- PDB
- 5ZLF
- Type
- protein
- Length
- 1,127 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
- B29, MG
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Octaprenyl diphosphate synthase (EC 2.5.1.90) | protein | 293 | 69% helix, 1% strand | P0AD57 |
| B | Octaprenyl diphosphate synthase (EC 2.5.1.90) | protein | 259 | 66% helix, 0% strand | P0AD57 |
| C | Octaprenyl diphosphate synthase (EC 2.5.1.90) | protein | 286 | 77% helix, 0% strand | P0AD57 |
| D | Octaprenyl diphosphate synthase (EC 2.5.1.90) | protein | 289 | 67% helix, 1% strand | P0AD57 |
Ligands and binding sites
- B29 · [2-(3-dibenzofuran-4-yl-phenyl)-1-hydroxy-1-phosphono-ethyl]-phosphonic acid · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.82 | 0.83 | 91 | B29, MG |
| 2 | 883 | 0.82 | 0.84 | 90 | MG |
| 3 | 316 | 0.66 | 0.81 | 36 | empty |
| 4 | 60 | 0.63 | 0.92 | 19 | empty |
| 5 | 225 | 0.61 | 0.81 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1842 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1767 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 251 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 64 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ZLF · CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH ligand… · 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 C 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 5ZLF · PDBe 5ZLF · UniProt P0AD57
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