MolNFT v2 · #46614 · protein
Crystal Structure of Bacteriophytochrome chromophore binding domain at 1.45 angstrom resolution
2O9C: “Crystal Structure of Bacteriophytochrome chromophore binding domain at 1.45 angstrom resolution”. X-ray diffraction at 1.45, 1 ligand (LBV), 4 pockets (best druggability 0.80). MolNFT v2 #46614 on GenesisL1: 3D structure, binding…
- PDB
- 2O9C
- Type
- protein
- Length
- 319 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Deinococcus radiodurans
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9RZA4
- Ligands
- LBV
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.45 · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 319 | 32% helix, 27% strand | Q9RZA4 |
Ligands and binding sites
- LBV · 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.80 | 0.91 | 41 | LBV |
| 2 | 60 | 0.57 | 0.90 | 19 | empty |
| 3 | 164 | 0.54 | 0.80 | 33 | empty |
| 4 | 73 | 0.43 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 1 cofactor (biliverdin attachment).
Compared structures
- 2O9C · Crystal structure of bacteriophytochrome chromophore binding domain at 1.45 ångström… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RZA4 · AlphaFold monomer V2.0 prediction for bacteriophytochrome (Q9RZA4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9RZA4
- Elsewhere: RCSB PDB 2O9C · PDBe 2O9C · UniProt Q9RZA4
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