Research workbench
Structure of the pfr form of a canonical phytochrome
Analyse Structure of the pfr form of a canonical phytochrome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C5K
- Type
- protein
- Length
- 1,926 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9RZA4
- Ligands
- BLA, BGC
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 490 | 36% helix, 24% strand | Q9RZA4 |
| B | Bacteriophytochrome (EC 2.7.13.3) | protein | 486 | 36% helix, 24% strand | Q9RZA4 |
| C | Bacteriophytochrome (EC 2.7.13.3) | protein | 476 | 37% helix, 24% strand | Q9RZA4 |
| D | Bacteriophytochrome (EC 2.7.13.3) | protein | 474 | 36% helix, 24% strand | Q9RZA4 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 4 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · chains C
- EDO · 1,2-ethanediol · additive · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.82 | 0.91 | 48 | BLA |
| 2 | 393 | 0.81 | 0.90 | 46 | BLA, ACT |
| 3 | 348 | 0.81 | 0.91 | 44 | BLA |
| 4 | 439 | 0.80 | 0.88 | 46 | BLA |
| 5 | 206 | 0.78 | 0.92 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1355 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1305 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 318 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 5C5K · PDBe 5C5K · UniProt Q9RZA4
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