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Egfp in neutral pH, directionality of optical properties of fluorescent proteins

Analyse Egfp in neutral pH, 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: 6YLQ
Type: protein
Length: 226 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Egfp
Ligands: CRO, MG
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Egfp	protein	226	12% helix, 52% strand	—

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 · chains A
MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · 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	98	0.76	0.97	25	CRO
2	71	0.35	0.77	13	empty

Modifications

Observed in the structure: 2 cofactor (chromophore).

Compared structures

6YLQ · EGFP in neutral pH, 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 6YLQ · PDBe 6YLQ

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