Research workbench
Crystal structure of the chromophore-binding domain of an unusual bacteriophytochrome RPBPHP3 from R. palustris
Analyse Crystal structure of the chromophore-binding domain of an unusual… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OOL
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor protein
- UniProt
- Q6N5G2
- Ligands
- LBV
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor protein | protein | 304 | 35% helix, 28% strand | Q6N5G2 |
| B | Sensor protein | protein | 298 | 32% helix, 29% strand | Q6N5G2 |
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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.80 | 0.83 | 80 | LBV |
| 2 | 489 | 0.79 | 0.86 | 57 | LBV |
| 3 | 288 | 0.64 | 0.81 | 35 | empty |
| 4 | 164 | 0.44 | 0.74 | 20 | empty |
| 5 | 81 | 0.40 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 2OOL · Crystal structure of the chromophore-binding domain of an unusual bacteriophytochrome… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6N5G2
- Elsewhere: RCSB PDB 2OOL · PDBe 2OOL · UniProt Q6N5G2
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