MolNFT v1 · #82857 · protein
Crystal structure of pcrb from bacillus subtilis subap. subtilis str. 168
3VZX · Heptaprenylglyceryl phosphate synthase: “Crystal structure of pcrb from bacillus subtilis subap. subtilis str. 168”. X-ray diffraction, 2 ligands (MG, CL), 6 pockets (best druggability 0.74). MolNFT v1 #82857 on GenesisL1: 3D…
- PDB
- 3VZX
- Type
- protein
- Length
- 455 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
- MG, CL
- Pockets
- 6 · best druggability 0.74
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 | 227 | 41% helix, 19% strand | O34790 |
| B | Heptaprenylglyceryl phosphate synthase (EC 2.5.1.-) | protein | 228 | 43% helix, 20% strand | O34790 |
Ligands and binding sites
- 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.74 | 0.86 | 38 | empty |
| 2 | 303 | 0.72 | 0.85 | 34 | CL |
| 3 | 65 | 0.60 | 0.90 | 21 | empty |
| 4 | 83 | 0.35 | 0.75 | 15 | empty |
| 5 | 76 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1280 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3VZX · Crystal structure of PcrB from bacillus subtilis subap. subtilis str. 168 · 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 3VZX · PDBe 3VZX · UniProt O34790
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