Research workbench
Crystal structure of coelenteramine-bound renilla reniformis luciferase RLUC8-D120A variant
Analyse Crystal structure of coelenteramine-bound renilla reniformis luciferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OMO
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Renilla reniformis luciferase RLUC8-D120A variant
- Ligands
- VKB, MG, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renilla reniformis luciferase RLUC8-D120A variant | protein | 308 | 45% helix, 17% strand | — |
| B | Renilla reniformis luciferase RLUC8-D120A variant | protein | 295 | 43% helix, 18% strand | — |
Ligands and binding sites
- VKB · 4-[5-azanyl-6-(phenylmethyl)pyrazin-2-yl]phenol · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.78 | 0.82 | 61 | CL |
| 2 | 297 | 0.72 | 0.85 | 44 | VKB, CL |
| 3 | 121 | 0.41 | 0.75 | 18 | empty |
| 4 | 64 | 0.40 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 419 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7OMO · Crystal structure of coelenteramine-bound Renilla reniformis luciferase RLuc8-D120A… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 7OMO · PDBe 7OMO
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