MolNFT v1 · #46603 · protein
Crystal structure of bacteriophytochrome chromophore binding domain
2O9B: “Crystal structure of bacteriophytochrome chromophore binding domain”. X-ray diffraction, 1 ligand (LBV), 4 pockets (best druggability 0.80). MolNFT v1 #46603 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2O9B
- 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 0.80
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 315 | 30% 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 | 287 | 0.80 | 0.91 | 34 | LBV |
| 2 | 92 | 0.53 | 0.84 | 25 | empty |
| 3 | 145 | 0.51 | 0.79 | 30 | empty |
| 4 | 78 | 0.40 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor (biliverdin attachment).
Compared structures
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 2O9B · PDBe 2O9B · UniProt Q9RZA4
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