MolNFT v1 · #82859 · protein
Crystal structure of pcrb complexed with fspp from bacillus subtilis subap. subtilis str. 168
3VZZ · Heptaprenylglyceryl phosphate synthase: “Crystal structure of pcrb complexed with fspp from bacillus subtilis subap. subtilis str. 168”. X-ray diffraction, 3 ligands (FPS, MG, CL), 5 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 3VZZ
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heptaprenylglyceryl phosphate synthase
- EC
- 2.5.1.-
- UniProt
- O34790
- Ligands
- FPS, MG, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heptaprenylglyceryl phosphate synthase (EC 2.5.1.-) | protein | 226 | 40% helix, 19% strand | O34790 |
| B | Heptaprenylglyceryl phosphate synthase (EC 2.5.1.-) | protein | 228 | 43% helix, 19% strand | O34790 |
Ligands and binding sites
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.78 | 0.88 | 52 | FPS |
| 2 | 295 | 0.70 | 0.85 | 39 | empty |
| 3 | 79 | 0.35 | 0.76 | 15 | empty |
| 4 | 69 | 0.32 | 0.74 | 16 | empty |
| 5 | 55 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1284 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3VZZ · Crystal structure of PcrB complexed with FsPP from bacillus subtilis subap. subtilis str.… · the same entry in another collection · chain A against A, TM-score 1.00
- O34790 · AlphaFold monomer V2.0 prediction for heptaprenylglyceryl phosphate synthase (O34790) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O34790
- Elsewhere: RCSB PDB 3VZZ · PDBe 3VZZ · UniProt O34790
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