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Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and ipp bound
Analyse Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EZ3
- Type
- protein
- Length
- 1,419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase, putative
- UniProt
- A5K4U6
- Ligands
- ZOL, IPE, MG
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase, putative | protein | 358 | 71% helix, 1% strand | A5K4U6 |
| B | Farnesyl pyrophosphate synthase, putative | protein | 353 | 72% helix, 1% strand | A5K4U6 |
| C | Farnesyl pyrophosphate synthase, putative | protein | 357 | 71% helix, 1% strand | A5K4U6 |
| D | Farnesyl pyrophosphate synthase, putative | protein | 351 | 73% helix, 1% strand | A5K4U6 |
Ligands and binding sites
- ZOL · Zoledronic acid · ligand · 4 copies · chains A, B, C, D
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.81 | 0.88 | 64 | ZOL, IPE, MG, GOL |
| 2 | 497 | 0.80 | 0.88 | 69 | ZOL, IPE, MG, GOL, EDO |
| 3 | 534 | 0.80 | 0.86 | 70 | ZOL, IPE, MG, GOL |
| 4 | 526 | 0.80 | 0.86 | 73 | ZOL, IPE, MG |
| 5 | 224 | 0.62 | 0.82 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3605 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 3588 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 393 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 376 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 144 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3EZ3 · Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040… · 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 3EZ3 · PDBe 3EZ3 · UniProt A5K4U6
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