MolNFT v1 · #121167 · protein
Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph-1182
5HN8 · Farnesyl pyrophosphate synthase, putative: “Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph-1182”. X-ray diffraction, 2 ligands (HXK, SO4), 17 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 5HN8
- Type
- protein
- Length
- 1,315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase, putative
- UniProt
- A5K4U6
- Ligands
- HXK, SO4
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase, putative | protein | 321 | 69% helix, 1% strand | A5K4U6 |
| B | Farnesyl pyrophosphate synthase, putative | protein | 326 | 71% helix, 1% strand | A5K4U6 |
| C | Farnesyl pyrophosphate synthase, putative | protein | 334 | 71% helix, 1% strand | A5K4U6 |
| D | Farnesyl pyrophosphate synthase, putative | protein | 334 | 72% helix, 1% strand | A5K4U6 |
Ligands and binding sites
- HXK · 2-{[3-hydroxy-5-(octyloxy)benzyl]sulfanyl}benzoic acid · ligand · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.75 | 0.78 | 99 | empty |
| 2 | 549 | 0.74 | 0.81 | 64 | HXK |
| 3 | 587 | 0.74 | 0.81 | 62 | HXK |
| 4 | 682 | 0.73 | 0.79 | 66 | HXK |
| 5 | 126 | 0.73 | 0.93 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3505 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 3369 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 327 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5HN8 · Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with… · 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 5HN8 · PDBe 5HN8 · UniProt A5K4U6
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