Research workbench
Crystal structure of green fluorescent protein from zoanthus sp at 2.2 a resolution
Analyse Crystal structure of green fluorescent protein from zoanthus sp at 2.2 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OJK
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-like fluorescent chromoprotein FP506
- UniProt
- Q9U6Y5
- Ligands
- NYG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GFP-like fluorescent chromoprotein FP506 | protein | 225 | 5% helix, 56% strand | Q9U6Y5 |
Ligands and binding sites
- NYG · [(4Z)-2-[(1S)-1,3-diamino-3-oxopropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.74 | 0.97 | 27 | NYG |
| 2 | 76 | 0.73 | 0.97 | 26 | NYG |
| 3 | 170 | 0.52 | 0.79 | 35 | empty |
| 4 | 86 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 624 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2OJK · Crystal Structure of Green Fluorescent Protein from Zoanthus sp at 2.2 A Resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U6Y5 · AlphaFold monomer V2.0 prediction for GFP-like fluorescent chromoprotein FP506 (Q9U6Y5) · a predicted model of the same protein · chain B 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 Q9U6Y5
- Elsewhere: RCSB PDB 2OJK · PDBe 2OJK · UniProt Q9U6Y5
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