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Variations on the GFP chromophore scaffold: a fragmented 5-membered heterocycle revealed in the 2.1A crystal structure of a non- fluorescent chromoprotein

Analyse Variations on the GFP chromophore scaffold: a fragmented 5-membered heterocycle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XQM
Type: protein
Length: 227 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kindling fluorescent protein
Ligands: CH6
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kindling fluorescent protein	protein	227	6% helix, 56% strand	—

Ligands and binding sites

CH6 · {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains A
ACY · Acetic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.75	0.98	26	CH6

Modifications

Observed in the structure: 1 cofactor (chromophore).

Compared structures

1XQM · Variations on the GFP chromophore scaffold: A fragmented 5-membered heterocycle revealed… · 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 1XQM · PDBe 1XQM

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