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A non-invasive GFP-based biosensor for mercury ions

Analyse A non-invasive GFP-based biosensor for mercury ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OKY
Type: protein
Length: 440 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CRO
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Green fluorescent protein	protein	220	9% helix, 54% strand	P42212

Ligands and binding sites

CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-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

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	109	0.78	0.97	31	CRO
2	104	0.77	0.97	28	CRO
3	210	0.50	0.76	28	empty
4	186	0.48	0.76	28	empty
5	95	0.35	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 989 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

2OKY · A non-invasive GFP-based biosensor for mercury ions · the same entry in another collection · chain B against B, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · 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 P42212
Elsewhere: RCSB PDB 2OKY · PDBe 2OKY · UniProt P42212

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