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Crystal structure of pcrb complexed with G1P from bacillus subtilis subap. subtilis str. 168
Analyse Crystal structure of pcrb complexed with G1P from bacillus subtilis subap.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZY
- 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
- 1GP, MG, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heptaprenylglyceryl phosphate synthase (EC 2.5.1.-) | protein | 226 | 41% helix, 19% strand | O34790 |
| B | Heptaprenylglyceryl phosphate synthase (EC 2.5.1.-) | protein | 228 | 43% helix, 21% strand | O34790 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · chains B
- MG · Magnesium ion · metal · 10 copies · chains A, B
- CL · Chloride ion · ion · 5 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 | 398 | 0.77 | 0.86 | 56 | 1GP |
| 2 | 323 | 0.73 | 0.85 | 43 | MG, CL |
| 3 | 92 | 0.37 | 0.75 | 15 | empty |
| 4 | 59 | 0.33 | 0.77 | 15 | empty |
| 5 | 73 | 0.33 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1264 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3VZY · Crystal structure of PcrB complexed with G1P 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 3VZY · PDBe 3VZY · UniProt O34790
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