MolNFT v1 · #121168 · protein
Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph-1186
5HN9 · Farnesyl pyrophosphate synthase, putative: “Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph-1186”. X-ray diffraction, 1 ligand (04W), 18 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5HN9
- Type
- protein
- Length
- 1,388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase, putative
- UniProt
- A5K4U6
- Ligands
- 04W
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase, putative | protein | 351 | 73% helix, 1% strand | A5K4U6 |
| B | Farnesyl pyrophosphate synthase, putative | protein | 356 | 73% helix, 1% strand | A5K4U6 |
| C | Farnesyl pyrophosphate synthase, putative | protein | 334 | 73% helix, 1% strand | A5K4U6 |
| D | Farnesyl pyrophosphate synthase, putative | protein | 347 | 73% helix, 1% strand | A5K4U6 |
Ligands and binding sites
- 04W · 2-{[3-(decyloxy)benzyl]oxy}-5-nitrobenzoic 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
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.83 | 0.90 | 67 | 04W |
| 2 | 538 | 0.83 | 0.89 | 72 | 04W |
| 3 | 633 | 0.81 | 0.86 | 74 | 04W |
| 4 | 619 | 0.81 | 0.86 | 80 | 04W |
| 5 | 77 | 0.73 | 0.96 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3547 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 3319 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 334 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 272 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HN9 · 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 5HN9 · PDBe 5HN9 · UniProt A5K4U6
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