Research workbench
Crystal structure of the luciferase complexed with substrate analogue
Analyse Crystal structure of the luciferase complexed with substrate analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DWV
- Type
- protein
- Length
- 431 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Luciferin 4-monooxygenase
- EC
- 1.13.12.7
- UniProt
- P08659
- Ligands
- 5J4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 431 | 32% helix, 23% strand | P08659 |
Ligands and binding sites
- 5J4 · 2-[6-(cyclobuta-1,3-dien-1-ylamino)-1,3-benzothiazol-2-yl]-1,3-thiazol-4-ol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.72 | 0.90 | 35 | 5J4 |
| 2 | 63 | 0.33 | 0.76 | 13 | empty |
| 3 | 60 | 0.30 | 0.74 | 15 | empty |
| 4 | 55 | 0.28 | 0.75 | 16 | empty |
Compared structures
- 5DWV · Crystal structure of the Luciferase complexed with substrate analogue · 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 5DWV · PDBe 5DWV · UniProt P08659
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