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Crystal structure of the photosensory core module of bacteriophytochrome RPA3015 from R. palustris
Analyse Crystal structure of the photosensory core module of bacteriophytochrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S21
- Type
- protein
- Length
- 928 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
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (light-regulated signal transduction histidine kinase), PHYB1 | protein | 473 | 32% helix, 23% strand | Q6N5G3 |
| B | Bacteriophytochrome (light-regulated signal transduction histidine kinase), PHYB1 | protein | 455 | 29% 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
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.83 | 0.91 | 49 | BLA |
| 2 | 401 | 0.82 | 0.91 | 50 | BLA |
| 3 | 616 | 0.77 | 0.82 | 71 | empty |
| 4 | 681 | 0.71 | 0.78 | 53 | empty |
| 5 | 308 | 0.70 | 0.84 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1402 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 4S21 · Crystal structure of the photosensory core module of bacteriophytochrome RPA3015 from 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 4S21 · PDBe 4S21 · UniProt Q6N5G3
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