Research workbench
Crystal structure of renilla reniformis luciferase variant RLUC8- W121F/E144Q in complex with a coelenteramide (the postcatalytic enzyme-product complex)
Analyse Crystal structure of renilla reniformis luciferase variant RLUC8- W121F/E144Q… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YN2
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coelenterazine H 2-monooxygenase
- EC
- 1.13.12.5
- UniProt
- P27652
- Ligands
- CEI, K
- Pockets
- 3 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coelenterazine H 2-monooxygenase (EC 1.13.12.5) | protein | 310 | 45% helix, 18% strand | P27652 |
| B | Coelenterazine H 2-monooxygenase (EC 1.13.12.5) | protein | 309 | 42% helix, 18% strand | P27652 |
Ligands and binding sites
- CEI · N-[3-benzyl-5-(4-hydroxyphenyl)pyrazin-2-yl]-2-(4-hydroxyphenyl)acetamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains B
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.88 | 0.89 | 101 | CEI, ACT |
| 2 | 207 | 0.51 | 0.77 | 39 | empty |
| 3 | 192 | 0.51 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6YN2 · Crystal structure of Renilla reniformis luciferase variant RLuc8-W121F/E144Q in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P27652 · AlphaFold monomer V2.0 prediction for coelenterazine H 2-monooxygenase (P27652) · 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 P27652
- Elsewhere: RCSB PDB 6YN2 · PDBe 6YN2 · UniProt P27652
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.