Author Archives: Alexander Bond

Green Fluorescent Protein


Number of Polypeptide Chains in the Protein:   2

Chain Designation:  

Chain 1: A, B

Gene Names:  


PDB Deposition Title:  


Primary Citation Title:  

The molecular structure of green fluorescent protein.

Citation Authors:  

Yang, F., Moss, L.G., Phillips Jr., G.N.

Citation Journal:  

(1996) Nat.Biotechnol. 14: 1246-1251

Related PDB Entries:  

1B9C, 1BFP, 1C4F, 1CV7, 1EMA


Information for Chain A;  UniprotKB Accession Number:  P42212

Primary Structure

Length of the Chain (from Uniprot P42212):  238

FASTA Sequence for the chain (from Uniprot P42212):

>sp|P42212|GFP_AEQVI Green fluorescent protein OS=Aequorea victoria GN=GFP PE=1 SV=1

Secondary Structures (DSSP defined; from RCSB PDB)

Helical Structures:  Number of Helices:  6;  Percentage of Residues:  10

Beta Strands:  Number of Strands:  14;  Percentage of Residues:  49

Secondary Structure Map:


Tertiary Structure

Number of Domains Along Chain A:  1

CATH Domain IDs:  1glfA00

CATH Classes:  A00: Mainly Beta

CATH Architectures:  A00: Beta Barrel

CATH Topologies:  A00: Green Fluorescent Protein

Topological Diagrams:



Function and Ligand Binding Site

Excerpt from Abstract:

The crystal structure of recombinant wild-type green fluorescent protein (GFP) has been solved to a resolution of 1.9 A by multiwavelength anomalous dispersion phasing methods. The protein is in the shape of a cylinder, comprising 11 strands of beta-sheet with an alpha-helix inside and short helical segments on the ends of the cylinder. This motif, with beta-structure on the outside and alpha-helix on the inside, represents a new protein fold, which we have named the beta-can. Two protomers pack closely together to form a dimer in the crystal. The fluorophores are protected inside the cylinders, and their structures are consistent with the formation of aromatic systems made up of Tyr66 with reduction of its C alpha-C beta bond coupled with cyclization of the neighboring glycine and serine residues. The environment inside the cylinder explains the effects of many existing mutants of GFP and suggests specific side chains that could be modified to change the spectral properties of GFP. Furthermore, the identification of the dimer contacts may allow mutagenic control of the state of assembly of the protein.

Description of Function from Uniprot:

Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca2+-activated photoprotein aequorin.

Selected Molecular Function GO Terms:

GO ID: 0006091, Name: Generation of precursor metabolites and energy, Definition: The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.


GO ID: 0008218, Name: Bioluminescence, Definition: The production of light by certain enzyme-catalyzed reactions in cells.


GO ID: 0018298, Name: Protein-chromophore linkage, Definition: The covalent or noncovalent attachment of a chromophore to a protein.

EC Number:   N/A

EC Description:   


Major Organic Ligand:   N/A

Ligand Binding Residues:

Ser 65, Tyr 66, Gly 67

Ligand Binding Site: