Research workbench
PAS-GAF bidomain of Glycine max phytochromeA
Analyse PAS-GAF bidomain of Glycine max phytochromeA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TC7
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.13
- Source
- Glycine max
- Molecule
- Phytochrome
- UniProt
- B4YB07
- Ligands
- CYC
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.13 · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Phytochrome | protein | 317 | 38% helix, 26% strand | B4YB07 |
| BBB | Phytochrome | protein | 319 | 38% helix, 26% strand | B4YB07 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 2 copies · chains AAA, BBB
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains AAA, BBB
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 | 560 | 0.82 | 0.87 | 59 | CYC |
| 2 | 293 | 0.79 | 0.90 | 37 | CYC |
| 3 | 281 | 0.63 | 0.80 | 27 | empty |
| 4 | 211 | 0.55 | 0.78 | 28 | PEG |
| 5 | 232 | 0.54 | 0.77 | 35 | PEG |
Interfaces
1 interface between chains.
- AAA–BBB · 1508 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (phycocyanobilin attachment).
Compared structures
- B4YB07 · AlphaFold monomer V2.0 prediction for phytochrome a-2 (B4YB07) · a predicted model of the same protein · chain AAA against A, TM-score 0.94
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 B4YB07
- Elsewhere: RCSB PDB 6TC7 · PDBe 6TC7 · UniProt B4YB07
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