MolNFT v1 · #59605 · protein
Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome pabphp in the pfr state
3C2W: “Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome pabphp in the pfr state”. X-ray diffraction, 1 ligand (BLA), 20 pockets (best druggability 0.87). MolNFT v1 #59605 on GenesisL1: 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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