Research workbench
Crystal structure of the phr domain of cryptochrome 1 from arabidopsis thaliana with amppnp bound
Analyse Crystal structure of the phr domain of cryptochrome 1 from arabidopsis thaliana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U3D
- Type
- protein
- Length
- 485 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptochrome 1 apoprotein
- UniProt
- Q43125
- Ligands
- FAD, ANP, NDS, MG, CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cryptochrome 1 apoprotein | protein | 485 | 53% helix, 6% strand | Q43125 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- NDS · Ethyl dimethyl ammonio propane sulfonate · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.82 | 0.86 | 56 | FAD, ANP |
| 2 | 117 | 0.79 | 0.97 | 26 | empty |
| 3 | 194 | 0.49 | 0.76 | 39 | MG, NDS |
| 4 | 77 | 0.38 | 0.77 | 15 | empty |
| 5 | 53 | 0.29 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1U3D · Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q43125 · AlphaFold monomer V2.0 prediction for cryptochrome-1 (Q43125) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q43125
- Elsewhere: RCSB PDB 1U3D · PDBe 1U3D · UniProt Q43125
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