Research workbench

Crystal structure of fast switching M159T mutant of fluorescent protein dronpa (DRONPA2)

Analyse Crystal structure of fast switching M159T mutant of fluorescent protein dronpa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NQJ
Type: protein
Length: 878 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein dronpa
UniProt: Q5TLG6
Ligands: GYC
Pockets: 14 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 3% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein dronpa	protein	223	2% helix, 56% strand	Q5TLG6
B	Fluorescent protein dronpa	protein	217	3% helix, 57% strand	Q5TLG6
C	Fluorescent protein dronpa	protein	223	4% helix, 56% strand	Q5TLG6
D	Fluorescent protein dronpa	protein	215	3% helix, 58% strand	Q5TLG6

Ligands and binding sites

GYC · [(4Z)-2-[(1R)-1-amino-2-mercaptoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.82	0.83	124	empty
2	95	0.77	0.98	26	GYC
3	91	0.77	0.98	25	GYC
4	95	0.77	0.98	26	GYC
5	82	0.74	0.97	26	GYC

Interfaces

4 interfaces between chains.

C–D · 1237 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1232 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 828 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 824 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

6NQJ · Crystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2) · 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
Every structure of UniProt Q5TLG6
Elsewhere: RCSB PDB 6NQJ · PDBe 6NQJ · UniProt Q5TLG6

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.