MolNFT v1 · #84617 · protein
Structure of the Y263F mutant of the cyanobacterial phytochrome CPH1
3ZQ5 · Phytochrome-like protein CPH1: “Structure of the Y263F mutant of the cyanobacterial phytochrome CPH1”. X-ray diffraction, 3 ligands (CYC, NA, PO4), 4 pockets (best druggability 0.85). MolNFT v1 #84617 on GenesisL1: 3D structure…
- PDB
- 3ZQ5
- Type
- protein
- Length
- 517 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytochrome-like protein CPH1
- EC
- 2.7.13.3
- UniProt
- Q55168
- Ligands
- CYC, NA, PO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytochrome-like protein CPH1 (EC 2.7.13.3) | protein | 517 | 38% helix, 27% strand | Q55168 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 4 copies · chains A
- GOL · Glycerol · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.85 | 0.94 | 39 | CYC |
| 2 | 113 | 0.50 | 0.81 | 27 | empty |
| 3 | 120 | 0.48 | 0.79 | 19 | empty |
| 4 | 84 | 0.48 | 0.82 | 14 | ACT |
Modifications
Observed in the structure: 1 cofactor (phycocyanobilin attachment).
Compared structures
- 3ZQ5 · Structure of the Y263F mutant of the cyanobacterial phytochrome Cph1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q55168 · AlphaFold monomer V2.0 prediction for phytochrome-like protein CPH1 (Q55168) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q55168
- Elsewhere: RCSB PDB 3ZQ5 · PDBe 3ZQ5 · UniProt Q55168
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