Research workbench
Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome pabphp in the pfr state
Analyse Crystal structure of the photosensory core domain of P. aeruginosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C2W
- Type
- protein
- Length
- 3,808 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9HWR3
- Ligands
- BLA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 478 | 34% helix, 25% strand | Q9HWR3 |
| B | Bacteriophytochrome (EC 2.7.13.3) | protein | 468 | 34% helix, 24% strand | Q9HWR3 |
| C | Bacteriophytochrome (EC 2.7.13.3) | protein | 482 | 32% helix, 25% strand | Q9HWR3 |
| D | Bacteriophytochrome (EC 2.7.13.3) | protein | 478 | 32% helix, 25% strand | Q9HWR3 |
| E | Bacteriophytochrome (EC 2.7.13.3) | protein | 471 | 30% helix, 25% strand | Q9HWR3 |
| F | Bacteriophytochrome (EC 2.7.13.3) | protein | 469 | 31% helix, 25% strand | Q9HWR3 |
| G | Bacteriophytochrome (EC 2.7.13.3) | protein | 482 | 31% helix, 25% strand | Q9HWR3 |
| H | Bacteriophytochrome (EC 2.7.13.3) | protein | 480 | 32% helix, 25% strand | Q9HWR3 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.87 | 0.88 | 99 | BLA |
| 2 | 405 | 0.84 | 0.92 | 46 | BLA |
| 3 | 398 | 0.84 | 0.92 | 43 | BLA |
| 4 | 852 | 0.84 | 0.86 | 76 | empty |
| 5 | 1092 | 0.83 | 0.84 | 105 | empty |
Interfaces
20 interfaces between chains.
- E–F · 2167 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2126 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2125 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2007 Ų buried · 21 hydrogen bonds · protein-protein
- D–H · 1526 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (biliverdin attachment).
Compared structures
- 3C2W · Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9HWR3 · AlphaFold monomer V2.0 prediction for bacteriophytochrome (Q9HWR3) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 Q9HWR3
- Elsewhere: RCSB PDB 3C2W · PDBe 3C2W · UniProt Q9HWR3
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