MolNFT v1 · #60022 · protein
Photoswitchable red fluorescent protein psrfp, on-state
3CFF · GFP-like photoswitchable fluorescent protein: “Photoswitchable red fluorescent protein psrfp, on-state”. X-ray diffraction, 1 ligand (NRQ), 16 pockets (best druggability 0.87). MolNFT v1 #60022 on GenesisL1: 3D structure, binding…
- PDB
- 3CFF
- 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
- 16 · 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
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.87 | 0.88 | 115 | empty |
| 2 | 93 | 0.75 | 0.97 | 33 | NRQ |
| 3 | 78 | 0.75 | 0.98 | 28 | NRQ |
| 4 | 91 | 0.75 | 0.97 | 30 | NRQ |
| 5 | 77 | 0.74 | 0.98 | 28 | NRQ |
Interfaces
18 interfaces between chains.
- S–H · 2169 Ų buried · 39 hydrogen bonds · protein-protein
- M–B · 2125 Ų buried · 39 hydrogen bonds · protein-protein
- L–A · 2095 Ų buried · 40 hydrogen bonds · protein-protein
- R–G · 2094 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1710 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 cofactor (artifact, chromophore).
Compared structures
- 3CFF · Photoswitchable red fluorescent protein psRFP, on-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 3CFF · PDBe 3CFF
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