MolNFT v1 · #178962 · protein
Real time reaction intermediates in stigmatella bacteriophytochrome P2
7JR5 · Photoreceptor-histidine kinase bphp: “Real time reaction intermediates in stigmatella bacteriophytochrome P2”. X-ray diffraction, 2 ligands (VHG, BEN), 14 pockets (best druggability 0.84). MolNFT v1 #178962 on GenesisL1: 3D…
- PDB
- 7JR5
- 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
- VHG, BEN
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Photoreceptor-histidine kinase bphp | protein | 482 | 24% helix, 8% strand | Q09E27 |
Ligands and binding sites
- VHG · 3-[2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-5-[[(3~{S})-4-ethyl-3-methyl-2-oxidanylidene-1,3-dihydropyrrol-5-yl]methyl]-4-methyl-1~{H}-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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.84 | 0.94 | 43 | VHG |
| 2 | 449 | 0.82 | 0.89 | 53 | VHG |
| 3 | 404 | 0.74 | 0.84 | 38 | BEN |
| 4 | 70 | 0.71 | 0.95 | 21 | empty |
| 5 | 364 | 0.68 | 0.82 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 1668 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7JR5 · Real Time Reaction Intermediates in Stigmatella Bacteriophytochrome P2 · the same entry in another collection · chain A against A, 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 7JR5 · PDBe 7JR5 · UniProt Q09E27
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