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Crystal structure of P. vivax geranylgeranyl diphosphate synthase complexed with bph-811
Analyse Crystal structure of P. vivax geranylgeranyl diphosphate synthase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RYW
- Type
- protein
- Length
- 1,427 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- UniProt
- A5K4U6
- Ligands
- K9H, MG, SO4
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Farnesyl pyrophosphate synthase | protein | 358 | 71% helix, 1% strand | A5K4U6 |
| B | Farnesyl pyrophosphate synthase | protein | 356 | 72% helix, 1% strand | A5K4U6 |
| C | Farnesyl pyrophosphate synthase | protein | 355 | 72% helix, 1% strand | A5K4U6 |
Ligands and binding sites
- K9H · {2-[5-(decyloxy)pyridin-3-yl]ethane-1,1-diyl}bis(phosphonic acid) · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
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 | 941 | 0.89 | 0.91 | 135 | K9H, MG, SO4 |
| 2 | 1052 | 0.88 | 0.89 | 135 | K9H, MG, SO4 |
| 3 | 936 | 0.76 | 0.79 | 76 | empty |
| 4 | 79 | 0.74 | 0.97 | 18 | empty |
| 5 | 473 | 0.70 | 0.81 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–D · 3628 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 3537 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 406 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 329 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 210 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3RYW · Crystal structure of P. vivax geranylgeranyl diphosphate synthase complexed with BPH-811 · 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 3RYW · PDBe 3RYW · UniProt A5K4U6
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