Research workbench
High-resolution crystal structures of transient intermediates in the phytochrome photocycle, 33 ms structure
Analyse High-resolution crystal structures of transient intermediates in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JRI
- Type
- protein
- Length
- 964 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photoreceptor-histidine kinase bphp
- UniProt
- Q09E27
- Ligands
- 3Q8, BEN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Photoreceptor-histidine kinase bphp | protein | 482 | 26% helix, 11% strand | Q09E27 |
Ligands and binding sites
- 3Q8 · 3-[2-[[5-[[(3E,4S)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · 2 copies · chains A, B
- BEN · Benzamidine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.83 | 0.90 | 51 | 3Q8 |
| 2 | 454 | 0.83 | 0.90 | 45 | 3Q8 |
| 3 | 446 | 0.73 | 0.83 | 42 | BEN |
| 4 | 338 | 0.62 | 0.79 | 42 | empty |
| 5 | 164 | 0.60 | 0.83 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1626 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7JRI · High-resolution Crystal Structures of Transient Intermediates in the Phytochrome… · the same entry in another collection · chain B against B, 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 Q09E27
- Elsewhere: RCSB PDB 7JRI · PDBe 7JRI · UniProt Q09E27
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