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Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic thermotoga maritima V73Y mutant
Analyse Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V4J
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Octoprenyl-diphosphate synthase
- EC
- 2.5.1.11
- UniProt
- Q9X1M1
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Octoprenyl-diphosphate synthase (EC 2.5.1.11) | protein | 280 | 74% helix, 1% strand | Q9X1M1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.79 | 0.84 | 73 | SO4 |
| 2 | 578 | 0.72 | 0.80 | 57 | SO4 |
| 3 | 54 | 0.71 | 0.98 | 14 | empty |
| 4 | 65 | 0.69 | 0.96 | 14 | empty |
| 5 | 240 | 0.57 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1727 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1V4J · Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9X1M1
- Elsewhere: RCSB PDB 1V4J · PDBe 1V4J · UniProt Q9X1M1
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