MolNFT v1 · #78392 · protein
Crystal structure of the infrared fluorescent D207H variant of deinococcus bacteriophytochrome chromophore binding domain at 1.24 ångström resolution
3S7O: “Crystal structure of the infrared fluorescent D207H variant of deinococcus bacteriophytochrome chromophore…”. X-ray diffraction, 1 ligand (LBV), 5 pockets (best druggability 0.79). MolNFT v1 #78392 on GenesisL1: 3D structure…
- PDB
- 3S7O
- 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
- 5 · 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
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.79 | 0.90 | 44 | LBV |
| 2 | 112 | 0.52 | 0.82 | 27 | empty |
| 3 | 137 | 0.50 | 0.79 | 34 | empty |
| 4 | 72 | 0.41 | 0.79 | 15 | empty |
| 5 | 59 | 0.35 | 0.78 | 22 | empty |
Compared structures
- 3S7O · 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 3S7O · PDBe 3S7O · UniProt Q9RZA4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.