Research workbench
Crystal structure of monomeric photosensitizing fluorescent protein, supernova
Analyse Crystal structure of monomeric photosensitizing fluorescent protein, supernova in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WCK
- Type
- protein
- Length
- 1,741 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monomeric photosenitizing fluorescent protein supernova
- Ligands
- CRQ
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, H | Monomeric photosenitizing fluorescent protein supernova | protein | 217 | 7% helix, 54% strand | — |
| C | Monomeric photosenitizing fluorescent protein supernova | protein | 220 | 7% helix, 53% strand | — |
| F | Monomeric photosenitizing fluorescent protein supernova | protein | 217 | 7% helix, 54% strand | — |
| G | Monomeric photosenitizing fluorescent protein supernova | protein | 219 | 8% helix, 54% strand | — |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.81 | 0.98 | 37 | CRQ |
| 2 | 138 | 0.81 | 0.98 | 35 | CRQ |
| 3 | 132 | 0.81 | 0.98 | 37 | CRQ |
| 4 | 137 | 0.81 | 0.97 | 33 | CRQ |
| 5 | 136 | 0.81 | 0.97 | 38 | CRQ |
Interfaces
12 interfaces between chains.
- A–B · 1214 Ų buried · 1 hydrogen bond · protein-protein
- D–H · 1189 Ų buried · 1 hydrogen bond · protein-protein
- E–G · 1160 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 895 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 825 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 3WCK · Crystal structure of monomeric photosensitizing fluorescent protein, Supernova · 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 3WCK · PDBe 3WCK
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