MolNFT v1 · #162210 · protein
Crystallographic superstructure of the photosensory core module (pas- gaf-phy) of the bacterial phytochrome AGP1 (ATBPHP1) locked in a pr- like state
6R27 · Bacteriophytochrome protein: “Crystallographic superstructure of the photosensory core module (pas- gaf-phy) of the bacterial phytochrome…”. X-ray diffraction, 1 ligand (JQ2), 20 pockets (best druggability 0.84). MolNFT v1 #162210…
- PDB
- 6R27
- Type
- protein
- Length
- 1,876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome protein
- UniProt
- Q7CY45
- Ligands
- JQ2
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome protein | protein | 472 | 34% helix, 23% strand | Q7CY45 |
| B | Bacteriophytochrome protein | protein | 466 | 34% helix, 23% strand | Q7CY45 |
| C | Bacteriophytochrome protein | protein | 475 | 34% helix, 24% strand | Q7CY45 |
| D | Bacteriophytochrome protein | protein | 463 | 34% helix, 24% strand | Q7CY45 |
Ligands and binding sites
- JQ2 · 3-[2-[(~{Z})-[12-ethyl-6-(3-hydroxy-3-oxopropyl)-13-methyl-11-oxidanylidene-4,10-diazatricyclo[8.3.0.0^{3, 7}]trideca-1,3,6,12-tetraen-5-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.84 | 0.86 | 87 | empty |
| 2 | 290 | 0.80 | 0.91 | 36 | JQ2 |
| 3 | 391 | 0.79 | 0.88 | 63 | JQ2 |
| 4 | 349 | 0.79 | 0.89 | 45 | JQ2 |
| 5 | 344 | 0.79 | 0.89 | 50 | JQ2 |
Interfaces
6 interfaces between chains.
- A–B · 1650 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1643 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 640 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 225 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 201 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified, 4 covalent (engineered, covalent ligand).
Compared structures
- 6R27 · Crystallographic superstructure of the photosensory core module (PAS-GAF-PHY) of the… · 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 Q7CY45
- Elsewhere: RCSB PDB 6R27 · PDBe 6R27 · UniProt Q7CY45
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