Research workbench
Crystal structure of monomeric reversibly photoswitchable red fluorescent protein rstagrfp in the on state
Analyse Crystal structure of monomeric reversibly photoswitchable red fluorescent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U8C
- Type
- protein
- Length
- 892 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein rstagrfp
- Ligands
- NRQ
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fluorescent protein rstagrfp | protein | 223 | 4% helix, 57% 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 A, B, C, D
- GOL · Glycerol · additive · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.86 | 0.92 | 52 | empty |
| 2 | 114 | 0.77 | 0.97 | 32 | NRQ |
| 3 | 121 | 0.77 | 0.96 | 35 | NRQ |
| 4 | 103 | 0.76 | 0.96 | 32 | NRQ |
| 5 | 105 | 0.75 | 0.96 | 33 | NRQ |
Interfaces
6 interfaces between chains.
- A–D · 1531 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1511 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 911 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 110 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 3U8C · Crystal structure of monomeric reversibly photoswitchable red fluorescent protein… · 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
- Elsewhere: RCSB PDB 3U8C · PDBe 3U8C
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