Research workbench
Crystal structure of red fluorescent gene-engineered variant with improved folding - LANRFP_DELS83 (branchiostoma lanceolatum)
Analyse Crystal structure of red fluorescent gene-engineered variant with improved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JGE
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Red fluorescent protein blfp-R5
- UniProt
- B1PND0
- Ligands
- CR2
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Red fluorescent protein blfp-R5 | protein | 215 | 9% helix, 56% strand | B1PND0 |
| B | Red fluorescent protein blfp-R5 | protein | 216 | 9% helix, 55% strand | B1PND0 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.61 | 0.83 | 28 | empty |
| 2 | 80 | 0.36 | 0.76 | 17 | GOL |
| 3 | 80 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1029 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (chromophore).
Compared structures
- 4JGE · Crystal structure of red fluorescent gene-engineered variant with improved folding… · 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
- Every structure of UniProt B1PND0
- Elsewhere: RCSB PDB 4JGE · PDBe 4JGE · UniProt B1PND0
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