Research workbench
Photinus pyralis luciferase in the adenylate-forming conformation bound to dlsa
Analyse Photinus pyralis luciferase in the adenylate-forming conformation bound to dlsa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G36
- Type
- protein
- Length
- 1,065 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
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 522 | 31% helix, 22% strand | P08659 |
| B | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 543 | 31% helix, 24% strand | P08659 |
Ligands and binding sites
- SLU · 5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.82 | 0.84 | 107 | SLU |
| 2 | 1023 | 0.82 | 0.83 | 113 | SLU |
| 3 | 1049 | 0.79 | 0.80 | 97 | empty |
| 4 | 191 | 0.49 | 0.75 | 30 | empty |
| 5 | 51 | 0.48 | 0.86 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 430 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4G36 · Photinus pyralis luciferase in the adenylate-forming conformation bound to DLSA · 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 0.98
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 P08659
- Elsewhere: RCSB PDB 4G36 · PDBe 4G36 · UniProt P08659
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