Research workbench
Structure of cross-linked firefly luciferase in second catalytic conformation
Analyse Structure of cross-linked firefly luciferase in second catalytic conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G37
- Type
- protein
- Length
- 1,072 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Luciferin 4-monooxygenase
- EC
- 1.13.12.7
- UniProt
- P08659
- Ligands
- SLU, XLX, SO4, CL
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 533 | 32% helix, 26% strand | P08659 |
| B | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 539 | 32% helix, 25% strand | P08659 |
Ligands and binding sites
- SLU · 5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine · ligand · 2 copies · chains A, B
- XLX · 4,4'-(ethylenediimino)bis[4-oxobutyrate] · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.83 | 0.84 | 113 | SLU |
| 2 | 1084 | 0.81 | 0.82 | 117 | SLU, XLX |
| 3 | 147 | 0.75 | 0.92 | 26 | empty |
| 4 | 582 | 0.66 | 0.76 | 73 | empty |
| 5 | 547 | 0.64 | 0.76 | 63 | empty |
Interfaces
1 interface between chains.
- A–B · 738 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4G37 · Structure of cross-linked firefly luciferase in second catalytic conformation · the same entry in another collection · chain A against A, TM-score 1.00
- P08659 · AlphaFold monomer V2.0 prediction for luciferin 4-monooxygenase (P08659) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P08659
- Elsewhere: RCSB PDB 4G37 · PDBe 4G37 · UniProt P08659
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