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Crystal structure and raman studies of DSFP483, a cyan fluorescent protein from discosoma striata
Analyse Crystal structure and raman studies of DSFP483, a cyan fluorescent protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CGL
- Type
- protein
- Length
- 1,153 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-like fluorescent chromoprotein DSFP483
- UniProt
- Q9U6Y7
- Ligands
- CRQ, NA
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GFP-like fluorescent chromoprotein DSFP483 | protein | 223 | 5% helix, 56% strand | Q9U6Y7 |
| B | GFP-like fluorescent chromoprotein DSFP483 | protein | 217 | 3% helix, 57% strand | Q9U6Y7 |
| C | GFP-like fluorescent chromoprotein DSFP483 | protein | 220 | 5% helix, 56% strand | Q9U6Y7 |
| D | GFP-like fluorescent chromoprotein DSFP483 | protein | 219 | 5% helix, 57% strand | Q9U6Y7 |
| E | GFP-like fluorescent chromoprotein DSFP483 | protein | 214 | 5% helix, 56% strand | Q9U6Y7 |
| F | GFP-like fluorescent chromoprotein DSFP483 | protein | 60 | 7% helix, 23% strand | Q9U6Y7 |
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 · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 2 copies · chains A, C, B, 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 | 990 | 0.85 | 0.87 | 116 | NA |
| 2 | 154 | 0.82 | 0.98 | 30 | CRQ |
| 3 | 89 | 0.76 | 0.98 | 27 | CRQ |
| 4 | 93 | 0.76 | 0.98 | 26 | CRQ |
| 5 | 95 | 0.76 | 0.97 | 27 | CRQ |
Interfaces
9 interfaces between chains.
- B–D · 1222 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1211 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 960 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 949 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 471 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 cofactor (chromophore).
Compared structures
- 3CGL · Crystal Structure and Raman Studies of dsFP483, a Cyan Fluorescent Protein from Discosoma… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9U6Y7 · AlphaFold monomer V2.0 prediction for GFP-like fluorescent chromoprotein DSFP483 (Q9U6Y7) · a predicted model of the same protein · chain D 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
- Every structure of UniProt Q9U6Y7
- Elsewhere: RCSB PDB 3CGL · PDBe 3CGL · UniProt Q9U6Y7
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