Research workbench
Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor
Analyse Structure of a bacteriophytochrome and light-stimulated protomer swapping with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GW9
- Type
- protein
- Length
- 2,486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- B3Q7C0
- Ligands
- BLA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 628 | 32% helix, 22% strand | B3Q7C0 |
| B | Bacteriophytochrome (EC 2.7.13.3) | protein | 621 | 33% helix, 20% strand | B3Q7C0 |
| C | Bacteriophytochrome (EC 2.7.13.3) | protein | 622 | 34% helix, 21% strand | B3Q7C0 |
| D | Bacteriophytochrome (EC 2.7.13.3) | protein | 615 | 32% helix, 23% strand | B3Q7C0 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.83 | 0.91 | 46 | BLA |
| 2 | 350 | 0.82 | 0.92 | 46 | BLA |
| 3 | 306 | 0.82 | 0.92 | 43 | BLA |
| 4 | 359 | 0.81 | 0.90 | 46 | BLA |
| 5 | 1115 | 0.74 | 0.77 | 130 | empty |
Interfaces
2 interfaces between chains.
- A–D · 2238 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2064 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 modified, 4 cofactor (engineered, biliverdin attachment).
Compared structures
- 4GW9 · Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene… · 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 B3Q7C0
- Elsewhere: RCSB PDB 4GW9 · PDBe 4GW9 · UniProt B3Q7C0
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