Research workbench
Cryoem structure of arabidopsis thaliana phytochrome B
Analyse Cryoem structure of arabidopsis thaliana phytochrome B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RZW
- Type
- protein
- Length
- 1,723 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytochrome B
- UniProt
- P14713
- Ligands
- O6E
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytochrome B | protein | 859 | 36% helix, 23% strand | P14713 |
| B | Phytochrome B | protein | 864 | 37% helix, 21% strand | P14713 |
Ligands and binding sites
- O6E · 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.84 | 0.94 | 44 | O6E |
| 2 | 399 | 0.81 | 0.89 | 61 | O6E |
| 3 | 1031 | 0.75 | 0.78 | 76 | empty |
| 4 | 1051 | 0.75 | 0.77 | 83 | empty |
| 5 | 408 | 0.70 | 0.81 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 5075 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 P14713
- Elsewhere: RCSB PDB 7RZW · PDBe 7RZW · UniProt P14713
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