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Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph -703
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
- 3RBM
- Type
- protein
- Length
- 1,430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- UniProt
- A5K4U6
- Ligands
- B73, MG, SO4
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase | protein | 355 | 72% helix, 1% strand | A5K4U6 |
| B | Farnesyl pyrophosphate synthase | protein | 362 | 71% helix, 1% strand | A5K4U6 |
| C | Farnesyl pyrophosphate synthase | protein | 356 | 72% helix, 1% strand | A5K4U6 |
| D | Farnesyl pyrophosphate synthase | protein | 357 | 71% helix, 1% strand | A5K4U6 |
Ligands and binding sites
- B73 · 3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium · ligand · 4 copies · chains A, B, C, D
- 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.89 | 0.90 | 149 | MG, B73, SO4 |
| 2 | 1157 | 0.87 | 0.88 | 151 | MG, B73, SO4 |
| 3 | 58 | 0.69 | 0.96 | 17 | empty |
| 4 | 300 | 0.61 | 0.79 | 51 | empty |
| 5 | 234 | 0.60 | 0.80 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3587 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 3557 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 412 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3RBM · 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 3RBM · PDBe 3RBM · UniProt A5K4U6
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