MolNFT v1 · #46982 · protein

A non-invasive GFP-based biosensor for mercury ions

2OKW · Green fluorescent protein: “A non-invasive GFP-based biosensor for mercury ions”. X-ray diffraction, 1 ligand (CRO), 20 pockets (best druggability 0.78). MolNFT v1 #46982 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2OKW
Type: protein
Length: 1,320 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CRO
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Green fluorescent protein	protein	220	9% helix, 53% 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 · 6 copies · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.78	0.98	27	CRO
2	90	0.77	0.98	26	CRO
3	91	0.77	0.98	27	CRO
4	99	0.76	0.97	26	CRO
5	97	0.76	0.97	31	CRO

Interfaces

4 interfaces between chains.

A–B · 1040 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 985 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 977 Å² buried · 27 hydrogen bonds · protein-protein
B–E · 463 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 cofactor (chromophore).

Compared structures

2OKW · A non-invasive GFP-based biosensor for mercury ions · the same entry in another collection · chain F against F, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain D 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 2OKW · PDBe 2OKW · UniProt P42212

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