Research workbench
Crystal structure of the infrared fluorescent D207H variant of deinococcus bacteriophytochrome chromophore binding domain at 1.72 ångström resolution
Analyse Crystal structure of the infrared fluorescent D207H variant of deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S7P
- Type
- protein
- Length
- 315 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9RZA4
- Ligands
- LBV
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 315 | 32% helix, 28% 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 | 297 | 0.79 | 0.90 | 42 | LBV |
| 2 | 120 | 0.52 | 0.82 | 30 | empty |
| 3 | 144 | 0.51 | 0.79 | 31 | empty |
| 4 | 71 | 0.39 | 0.78 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor (biliverdin attachment).
Compared structures
- 3S7P · Crystal Structure of the Infrared Fluorescent D207H variant of Deinococcus… · 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 3S7P · PDBe 3S7P · UniProt Q9RZA4
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