Research workbench
Photoswitchable red fluorescent protein psrfp, off-state
Analyse Photoswitchable red fluorescent protein psrfp, off-state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CFH
- Type
- protein
- Length
- 896 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-like photoswitchable fluorescent protein
- Ligands
- NRQ
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M, R, S | GFP-like photoswitchable fluorescent protein | protein | 58 | 12% helix, 57% strand | — |
| A, B, G, H | GFP-like photoswitchable fluorescent protein | protein | 166 | 4% helix, 55% strand | — |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains L, A, M, B, R, G, S, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.87 | 0.88 | 113 | empty |
| 2 | 105 | 0.77 | 0.97 | 29 | NRQ |
| 3 | 84 | 0.76 | 0.98 | 23 | NRQ |
| 4 | 94 | 0.75 | 0.97 | 30 | NRQ |
| 5 | 81 | 0.74 | 0.98 | 26 | NRQ |
Interfaces
19 interfaces between chains.
- S–H · 2207 Ų buried · 39 hydrogen bonds · protein-protein
- M–B · 2132 Ų buried · 38 hydrogen bonds · protein-protein
- R–G · 2103 Ų buried · 36 hydrogen bonds · protein-protein
- L–A · 2099 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1719 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (artifact).
Compared structures
- 3CFH · Photoswitchable red fluorescent protein psRFP, off-state · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 3CFH · PDBe 3CFH
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