MolNFT v1 · #105494 · protein
Crystal structure of bacteriophytochrome RPBPHP2 from photosynthetic bacterium R. palustris
4R6L · Bacteriophytochrome (light-regulated signal transduction…: “Crystal structure of bacteriophytochrome RPBPHP2 from photosynthetic bacterium R. palustris”. X-ray diffraction, 1 ligand (BLA), 12 pockets (best druggability 0.83). MolNFT…
- PDB
- 4R6L
- Type
- protein
- Length
- 921 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome (light-regulated signal transduction histidine kinase), PHYB1
- UniProt
- Q6N5G3
- Ligands
- BLA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (light-regulated signal transduction histidine kinase), PHYB1 | protein | 473 | 31% helix, 25% strand | Q6N5G3 |
| B | Bacteriophytochrome (light-regulated signal transduction histidine kinase), PHYB1 | protein | 448 | 31% helix, 25% strand | Q6N5G3 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.83 | 0.92 | 49 | BLA |
| 2 | 373 | 0.82 | 0.90 | 54 | BLA |
| 3 | 1119 | 0.80 | 0.81 | 131 | empty |
| 4 | 602 | 0.75 | 0.82 | 54 | empty |
| 5 | 228 | 0.68 | 0.84 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1375 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 4R6L · Crystal structure of bacteriophytochrome RpBphP2 from photosynthetic bacterium R.… · 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 Q6N5G3
- Elsewhere: RCSB PDB 4R6L · PDBe 4R6L · UniProt Q6N5G3
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