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Crystal structure of far-red fluorescent protein EQFP650

Analyse Crystal structure of far-red fluorescent protein EQFP650 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EDO
Type: protein
Length: 436 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Far-red fluorescent protein EQFP650
Ligands: NRQ
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Far-red fluorescent protein EQFP650	protein	218	6% helix, 58% strand	—

Ligands and binding sites

NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	102	0.76	0.97	30	NRQ
2	84	0.75	0.98	27	NRQ
3	138	0.60	0.84	31	empty
4	149	0.43	0.75	24	empty

Interfaces

1 interface between chains.

A–B · 930 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

4EDO · Crystal structure of far-red fluorescent protein eqFP650 · 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 4EDO · PDBe 4EDO

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