MolNFT v1 · #100869 · protein
Pcrb from geobacillus kaustophilus, with bound G1P
4NAE · Heptaprenylglyceryl phosphate synthase: “Pcrb from geobacillus kaustophilus, with bound G1P”. X-ray diffraction, 1 ligand (1GP), 4 pockets (best druggability 0.74). MolNFT v1 #100869 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4NAE
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heptaprenylglyceryl phosphate synthase
- EC
- 2.5.1.-
- UniProt
- Q5L3C1
- Ligands
- 1GP
- Pockets
- 4 · 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 | 219 | 42% helix, 20% strand | Q5L3C1 |
| B | Heptaprenylglyceryl phosphate synthase | protein | 215 | 42% helix, 20% strand | Q5L3C1 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.74 | 0.83 | 56 | 1GP, PE4 |
| 2 | 444 | 0.71 | 0.81 | 52 | 1GP, PE4 |
| 3 | 71 | 0.38 | 0.78 | 15 | empty |
| 4 | 69 | 0.28 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1452 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4NAE · PcrB from Geobacillus kaustophilus, with bound G1P · the same entry in another collection · chain A against A, TM-score 1.00
- Q5L3C1 · AlphaFold monomer V2.0 prediction for heptaprenylglyceryl phosphate synthase (Q5L3C1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5L3C1
- Elsewhere: RCSB PDB 4NAE · PDBe 4NAE · UniProt Q5L3C1
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