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Structure of the red fluorescent protein mscarlet at pH 7.8

Analyse Structure of the red fluorescent protein mscarlet at pH 7.8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LK4
Type: protein
Length: 216 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mscarlet
Ligands: NRQ, PO4
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mscarlet	protein	216	6% helix, 57% 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 · chains A
PO4 · Phosphate ion · ion · chains A
PGE · Triethylene glycol · additive · 4 copies · chains A
PG4 · Tetraethylene glycol · additive · chains A
PEG · Di(hydroxyethyl)ether · 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	80	0.75	0.98	27	NRQ
2	72	0.38	0.78	19	PGE

Modifications

Observed in the structure: 2 cofactor (chromophore).

Compared structures

5LK4 · Structure of the Red Fluorescent Protein mScarlet at pH 7.8 · 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 5LK4 · PDBe 5LK4

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