Research workbench
Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase.
Analyse Constructing tailored isoprenoid products by structure-guided modification of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OPD
- Type
- protein
- Length
- 904 residues
- Chains
- 2
- 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
- Pockets
- 8 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Conserved archaeal protein (EC 1.3.1.83) | protein | 452 | 40% helix, 27% strand | Q4JA33 |
Ligands and binding sites
- GRG · Geranylgeranyl diphosphate · ligand · 6 copies · chains A, B
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.90 | 0.91 | 128 | FDA, GRG |
| 2 | 1045 | 0.88 | 0.89 | 112 | FDA, GRG |
| 3 | 303 | 0.68 | 0.83 | 38 | empty |
| 4 | 89 | 0.64 | 0.90 | 21 | empty |
| 5 | 69 | 0.41 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4OPD · 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 B 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 Q4JA33
- Elsewhere: RCSB PDB 4OPD · PDBe 4OPD · UniProt Q4JA33
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