Research workbench
Deinococcus radiodurans bphp pas-gaf-phy Y263F mutant, dark
Analyse Deinococcus radiodurans bphp pas-gaf-phy Y263F mutant, dark in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NWN
- Type
- protein
- Length
- 1,891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9RZA4
- Ligands
- LBV
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 478 | 35% helix, 24% strand | Q9RZA4 |
| B | Bacteriophytochrome (EC 2.7.13.3) | protein | 475 | 35% helix, 24% strand | Q9RZA4 |
| C | Bacteriophytochrome (EC 2.7.13.3) | protein | 469 | 35% helix, 24% strand | Q9RZA4 |
| D | Bacteriophytochrome (EC 2.7.13.3) | protein | 469 | 35% helix, 24% strand | Q9RZA4 |
Ligands and binding sites
- LBV · 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.81 | 0.90 | 51 | LBV |
| 2 | 368 | 0.81 | 0.90 | 48 | LBV |
| 3 | 395 | 0.78 | 0.87 | 50 | LBV |
| 4 | 376 | 0.77 | 0.87 | 45 | LBV |
| 5 | 357 | 0.67 | 0.81 | 53 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1392 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1359 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 426 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 346 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (biliverdin attachment).
Compared structures
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 Q9RZA4
- Elsewhere: RCSB PDB 5NWN · PDBe 5NWN · UniProt Q9RZA4
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