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Crystal structure of a reconstructed kaede-type red fluorescent protein, lea X121

Analyse Crystal structure of a reconstructed kaede-type red fluorescent protein, lea… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DXP
Type: protein
Length: 215 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lea X121 GFP-like proteins
Ligands: CR8, MG
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lea X121 GFP-like proteins	protein	215	4% helix, 58% strand	—

Ligands and binding sites

CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · chains A
MG · Magnesium ion · metal · 2 copies · 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	72	0.72	0.97	24	CR8
2	61	0.40	0.81	21	empty

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4DXP · Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA X121 · 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 4DXP · PDBe 4DXP

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