Research workbench
Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state.
Analyse Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G1Z
- Type
- protein
- Length
- 982 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.03
- Source
- Agrobacterium fabrum (strain C58 / ATCC 33970)
- Molecule
- Bacteriophytochrome protein
- EC
- 2.7.13.3
- UniProt
- A9CI81
- Ligands
- EL5, ETE, SO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.03 · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome protein (EC 2.7.13.3) | protein | 489 | 40% helix, 24% strand | A9CI81 |
| B | Bacteriophytochrome protein (EC 2.7.13.3) | protein | 493 | 40% helix, 23% strand | A9CI81 |
Ligands and binding sites
- EL5 · Biliverdin · ligand · 2 copies · chains A, B
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 14 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.82 | 0.89 | 62 | EL5 |
| 2 | 507 | 0.82 | 0.89 | 63 | EL5 |
| 3 | 442 | 0.59 | 0.75 | 46 | SO4 |
| 4 | 186 | 0.52 | 0.78 | 24 | empty |
| 5 | 107 | 0.52 | 0.82 | 21 | GOL |
Interfaces
1 interface between chains.
- A–B · 329 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6G1Z · Crystal structure of a fluorescence optimized bathy phytochrome PAIRFP2 derived from… · 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 A9CI81
- Elsewhere: RCSB PDB 6G1Z · PDBe 6G1Z · UniProt A9CI81
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.