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Crystal structure of yellow fluorescent protein from zoanthus sp. at 1.8 a resolution
Analyse Crystal structure of yellow fluorescent protein from zoanthus sp. at 1.8 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OGR
- Type
- protein
- Length
- 892 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein FP538
- UniProt
- Q9U6Y4
- Ligands
- CH7
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fluorescent protein FP538 | protein | 223 | 6% helix, 55% 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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.82 | 0.86 | 93 | empty |
| 2 | 106 | 0.78 | 0.98 | 28 | CH7 |
| 3 | 110 | 0.78 | 0.97 | 28 | CH7 |
| 4 | 99 | 0.77 | 0.98 | 25 | CH7 |
| 5 | 112 | 0.77 | 0.97 | 27 | CH7 |
Interfaces
6 interfaces between chains.
- A–C · 1165 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1130 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 771 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 756 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 22 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 2OGR · Crystal Structure of Yellow Fluorescent Protein from Zoanthus sp. at 1.8 A Resolution · the same entry in another collection · chain C against C, TM-score 1.00
- Q9U6Y4 · AlphaFold monomer V2.0 prediction for GFP-like fluorescent chromoprotein FP538 (Q9U6Y4) · a predicted model of the same protein · 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
- Every structure of UniProt Q9U6Y4
- Elsewhere: RCSB PDB 2OGR · PDBe 2OGR · UniProt Q9U6Y4
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