Research workbench
Pas-gaf fragment from deinococcus radiodurans phytochrome 1PS after photoexcitation
Analyse Pas-gaf fragment from deinococcus radiodurans phytochrome 1PS after… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T3U
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9RZA4
- Ligands
- LBV
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Bacteriophytochrome (EC 2.7.13.3) | protein | 315 | 31% helix, 28% strand | Q9RZA4 |
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 313 | 30% helix, 29% 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 · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.84 | 0.85 | 107 | LBV |
| 2 | 506 | 0.79 | 0.85 | 42 | LBV |
| 3 | 285 | 0.69 | 0.84 | 43 | empty |
| 4 | 141 | 0.54 | 0.81 | 34 | empty |
| 5 | 243 | 0.53 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- B–A · 1396 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 6T3U · PAS-GAF fragment from Deinococcus radiodurans phytochrome 1ps after photoexcitation · the same entry in another collection · chain B against B, TM-score 1.00
- Q9RZA4 · AlphaFold monomer V2.0 prediction for bacteriophytochrome (Q9RZA4) · a predicted model of the same protein · chain A 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 Q9RZA4
- Elsewhere: RCSB PDB 6T3U · PDBe 6T3U · UniProt Q9RZA4
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