MolNFT v1 · #102559 · protein
Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase.
4OPG · Conserved archaeal protein: “Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase.”. X-ray diffraction, 3 ligands (GRG, FDA, SO4), 3 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 4OPG
- Type
- protein
- Length
- 452 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved archaeal protein
- EC
- 1.3.1.83
- UniProt
- Q4JA33
- Ligands
- GRG, FDA, SO4
- Pockets
- 3 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved archaeal protein (EC 1.3.1.83) | protein | 452 | 40% helix, 27% strand | Q4JA33 |
Ligands and binding sites
- GRG · Geranylgeranyl diphosphate · ligand · 2 copies · chains A
- FDA · Dihydroflavine-adenine dinucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.88 | 0.89 | 119 | FDA, GRG |
| 2 | 76 | 0.33 | 0.75 | 19 | empty |
| 3 | 70 | 0.32 | 0.75 | 11 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4OPG · Constructing tailored isoprenoid products by structure-guided modification of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q4JA33 · AlphaFold monomer V2.0 prediction for digeranylgeranylglycerophospholipid reductase… · a predicted model of the same protein · 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 Q4JA33
- Elsewhere: RCSB PDB 4OPG · PDBe 4OPG · UniProt Q4JA33
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