Research workbench
Crystal structure of the thermostable japanese firefly luciferase complexed with oxyluciferin and AMP
Analyse Crystal structure of the thermostable japanese firefly luciferase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D1R
- Type
- protein
- Length
- 539 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
- P13129
- Ligands
- AMP, OLU
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 539 | 32% helix, 24% strand | P13129 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- OLU · 2-(6-hydroxy-1,3-benzothiazol-2-yl)-1,3-thiazol-4(5H)-one · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.83 | 0.84 | 110 | AMP, OLU |
| 2 | 77 | 0.55 | 0.86 | 20 | empty |
| 3 | 296 | 0.55 | 0.75 | 26 | empty |
| 4 | 104 | 0.41 | 0.77 | 26 | empty |
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2D1R · Crystal structure of the thermostable Japanese firefly Luciferase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P13129 · AlphaFold monomer V2.0 prediction for luciferin 4-monooxygenase (P13129) · 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 P13129
- Elsewhere: RCSB PDB 2D1R · PDBe 2D1R · UniProt P13129
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