Research workbench
Improved NADPH-dependent Blue Fluorescent Protein
Analyse Improved NADPH-dependent Blue Fluorescent Protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P19
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Vibrio vulnificus
- Molecule
- Putative blue fluorescent protein
- Ligands
- NDP
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.05 · 3 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative blue fluorescent protein | protein | 239 | 49% helix, 19% strand | — |
| B, C | Putative blue fluorescent protein | protein | 218 | 47% helix, 22% strand | — |
| D | Putative blue fluorescent protein | protein | 238 | 50% helix, 18% strand | — |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.84 | 0.85 | 61 | empty |
| 2 | 374 | 0.80 | 0.89 | 58 | NDP |
| 3 | 309 | 0.79 | 0.90 | 45 | NDP |
| 4 | 399 | 0.74 | 0.84 | 41 | NDP |
| 5 | 440 | 0.73 | 0.83 | 54 | NDP |
Interfaces
4 interfaces between chains.
- A–B · 1555 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1547 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1367 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1345 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3P19 · Improved NADPH-dependent blue fluorescent protein · 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 3P19 · PDBe 3P19
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