Research workbench

EGFP_IN_ACIDIC_ENV directionality of optical properties of fluorescent proteins

Analyse EGFP_IN_ACIDIC_ENV directionality of optical properties of fluorescent proteins in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YLP
Type: protein
Length: 226 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: EGFP_IN_ACIDIC_ENV
Ligands: GYS, PO4
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	EGFP_IN_ACIDIC_ENV	protein	226	12% helix, 51% strand	—

Ligands and binding sites

GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · chains A
PO4 · Phosphate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.77	0.97	27	GYS
2	75	0.40	0.79	17	empty

Modifications

Observed in the structure: 2 cofactor (chromophore).

Compared structures

6YLP · EGFP_in_Acidic_env Directionality of Optical Properties of Fluorescent Proteins · the same entry in another collection · 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
Elsewhere: RCSB PDB 6YLP · PDBe 6YLP

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