MolNFT v1 · #7778 · protein
Red fluorescent protein (FP583 or DSRED(CLONTECH)) from discosoma sp.
1GGX · Protein (fluorescent protein FP583): “Red fluorescent protein (FP583 or DSRED(CLONTECH)) from discosoma sp.”. X-ray diffraction, 1 ligand (CRQ), 9 pockets (best druggability 0.84). MolNFT v1 #7778 on GenesisL1: 3D structure, binding…
- PDB
- 1GGX
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (fluorescent protein FP583)
- UniProt
- Q9U6Y8
- Ligands
- CRQ
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (fluorescent protein FP583) | protein | 216 | 6% helix, 57% strand | Q9U6Y8 |
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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.84 | 0.85 | 104 | empty |
| 2 | 97 | 0.76 | 0.97 | 26 | CRQ |
| 3 | 94 | 0.75 | 0.96 | 29 | CRQ |
| 4 | 86 | 0.75 | 0.97 | 25 | CRQ |
| 5 | 87 | 0.73 | 0.96 | 29 | CRQ |
Interfaces
6 interfaces between chains.
- A–B · 1406 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1404 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1100 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1076 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 1GGX · Red fluorescent protein (FP583 or DSRED(CLONTECH)) from discosoma sp. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U6Y8 · AlphaFold monomer V2.0 prediction for red fluorescent protein DRFP583 (Q9U6Y8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9U6Y8
- Elsewhere: RCSB PDB 1GGX · PDBe 1GGX · UniProt Q9U6Y8
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