MolNFT v1 · #121169 · protein
Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph-1251
5HNA · Farnesyl pyrophosphate synthase, putative: “Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph-1251”. X-ray diffraction, 1 ligand (63D), 16 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5HNA
- Type
- protein
- Length
- 1,408 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase, putative
- UniProt
- A5K4U6
- Ligands
- 63D
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Farnesyl pyrophosphate synthase, putative | protein | 352 | 72% helix, 1% strand | A5K4U6 |
Ligands and binding sites
- 63D · 4-chloro-2-{[3-(decyloxy)-5-hydroxybenzyl]oxy}-5-sulfamoylbenzoic acid · ligand · 4 copies · chains A, B, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.84 | 0.86 | 86 | 63D |
| 2 | 739 | 0.83 | 0.87 | 79 | 63D |
| 3 | 662 | 0.83 | 0.87 | 83 | 63D |
| 4 | 708 | 0.83 | 0.87 | 78 | 63D |
| 5 | 86 | 0.74 | 0.96 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3558 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 3554 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 334 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 317 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 156 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HNA · 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 5HNA · PDBe 5HNA · UniProt A5K4U6
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