MolNFT v1 · #143825 · protein
Stigmatella aurantiaca bacterial phytochrome P1, pas-gaf-phy T289H mutant, room temperature structure
6BAY · Photoreceptor-histidine kinase bphp: “Stigmatella aurantiaca bacterial phytochrome P1, pas-gaf-phy T289H mutant, room temperature structure”. X-ray diffraction, 1 ligand (BLR), 20 pockets (best druggability 0.84). MolNFT v1 #143825…
- PDB
- 6BAY
- Type
- protein
- Length
- 1,510 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photoreceptor-histidine kinase bphp
- UniProt
- Q097N3
- Ligands
- BLR
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Photoreceptor-histidine kinase bphp | protein | 505 | 32% helix, 24% strand | Q097N3 |
| C | Photoreceptor-histidine kinase bphp | protein | 500 | 20% helix, 12% strand | Q097N3 |
Ligands and binding sites
- BLR · 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.84 | 0.85 | 82 | empty |
| 2 | 377 | 0.84 | 0.93 | 53 | BLR |
| 3 | 363 | 0.83 | 0.92 | 48 | BLR |
| 4 | 574 | 0.80 | 0.86 | 78 | BLR |
| 5 | 59 | 0.70 | 0.97 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1964 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 714 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6BAY · Stigmatella aurantiaca bacterial phytochrome P1, PAS-GAF-PHY T289H mutant, room… · 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 Q097N3
- Elsewhere: RCSB PDB 6BAY · PDBe 6BAY · UniProt Q097N3
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