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Crystal structure of plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate
Analyse Crystal structure of plasmodium vivax putative polyprenyl pyrophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CC9
- Type
- protein
- Length
- 1,371 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative farnesyl pyrophosphate synthase
- UniProt
- A5K4U6
- Ligands
- GRG, NA
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative farnesyl pyrophosphate synthase | protein | 344 | 72% helix, 1% strand | A5K4U6 |
| B | Putative farnesyl pyrophosphate synthase | protein | 358 | 71% helix, 1% strand | A5K4U6 |
| C | Putative farnesyl pyrophosphate synthase | protein | 332 | 71% helix, 1% strand | A5K4U6 |
| D | Putative farnesyl pyrophosphate synthase | protein | 337 | 70% helix, 1% strand | A5K4U6 |
Ligands and binding sites
- GRG · Geranylgeranyl diphosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.82 | 0.86 | 80 | GRG |
| 2 | 1195 | 0.79 | 0.81 | 125 | GRG |
| 3 | 713 | 0.75 | 0.81 | 75 | GRG |
| 4 | 397 | 0.73 | 0.84 | 54 | GRG |
| 5 | 399 | 0.63 | 0.78 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3545 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3465 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 311 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 142 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3CC9 · Crystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase in… · 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 3CC9 · PDBe 3CC9 · UniProt A5K4U6
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