MolNFT v1 · #155950 · protein
Crystal structure of zsyellow soaked by CU2+
6LOF · GFP-like fluorescent chromoprotein FP538: “Crystal structure of zsyellow soaked by CU2+”. X-ray diffraction, 1 ligand (CH7), 5 pockets (best druggability 0.78). MolNFT v1 #155950 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6LOF
- Type
- protein
- Length
- 447 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-like fluorescent chromoprotein FP538
- UniProt
- Q9U6Y4
- Ligands
- CH7
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | GFP-like fluorescent chromoprotein FP538 | protein | 61 | 11% helix, 54% strand | Q9U6Y4 |
| A, B | GFP-like fluorescent chromoprotein FP538 | protein | 162 | 3% helix, 56% strand | Q9U6Y4 |
| D | GFP-like fluorescent chromoprotein FP538 | protein | 62 | 11% helix, 53% strand | Q9U6Y4 |
Ligands and binding sites
- CH7 · [(4Z)-4-(4-hydroxybenzylidene)-5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.78 | 0.97 | 25 | CH7 |
| 2 | 102 | 0.76 | 0.97 | 27 | CH7 |
| 3 | 68 | 0.73 | 0.98 | 20 | empty |
| 4 | 61 | 0.31 | 0.75 | 16 | empty |
| 5 | 58 | 0.28 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–A · 2313 Ų buried · 54 hydrogen bonds · protein-protein
- D–B · 2294 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 1096 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
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 Q9U6Y4
- Elsewhere: RCSB PDB 6LOF · PDBe 6LOF · UniProt Q9U6Y4
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