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Crystal structure of Plasmodium vivax putative farnesyl pyrophosphate synthase (Pv092040)
Analyse Crystal structure of Plasmodium vivax putative farnesyl pyrophosphate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MAV
- Type
- protein
- Length
- 1,399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Plasmodium vivax
- Molecule
- Farnesyl pyrophosphate synthase
- UniProt
- A5K4U6
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.1 · 4 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase | protein | 348 | 73% helix, 1% strand | A5K4U6 |
| B | Farnesyl pyrophosphate synthase | protein | 345 | 70% helix, 1% strand | A5K4U6 |
| C | Farnesyl pyrophosphate synthase | protein | 350 | 70% helix, 1% strand | A5K4U6 |
| D | Farnesyl pyrophosphate synthase | protein | 356 | 72% helix, 1% strand | A5K4U6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.77 | 0.82 | 62 | SO4 |
| 2 | 588 | 0.76 | 0.82 | 62 | SO4 |
| 3 | 600 | 0.71 | 0.79 | 53 | empty |
| 4 | 544 | 0.70 | 0.80 | 45 | SO4 |
| 5 | 194 | 0.58 | 0.81 | 32 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3549 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 3478 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 263 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3MAV · Crystal structure of plasmodium vivax putative farnesyl pyrophosphate synthase (PV092040) · 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 A5K4U6
- Elsewhere: RCSB PDB 3MAV · PDBe 3MAV · UniProt A5K4U6
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