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Crystal structure of fast switching M159Q mutant of fluorescent protein dronpa (DRONPA2)

Analyse Crystal structure of fast switching M159Q 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: 7RRJ
Type: protein
Length: 1,744 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein dronpa
UniProt: Q5TLG6
Ligands: GYC
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 4% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein dronpa	protein	216	4% helix, 57% strand	Q5TLG6
B	Fluorescent protein dronpa	protein	214	5% helix, 58% strand	Q5TLG6
C	Fluorescent protein dronpa	protein	218	5% helix, 57% strand	Q5TLG6
D, F	Fluorescent protein dronpa	protein	222	5% helix, 56% strand	Q5TLG6
E	Fluorescent protein dronpa	protein	223	4% helix, 56% strand	Q5TLG6
G	Fluorescent protein dronpa	protein	215	4% helix, 58% strand	Q5TLG6
H	Fluorescent protein dronpa	protein	214	4% 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 · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1057	0.83	0.84	119	empty
2	1183	0.82	0.83	121	empty
3	103	0.78	0.98	28	GYC
4	89	0.76	0.98	29	GYC
5	82	0.75	0.98	27	GYC

Interfaces

11 interfaces between chains.

D–H · 1248 Å² buried · 16 hydrogen bonds · protein-protein
B–F · 1248 Å² buried · 13 hydrogen bonds · protein-protein
C–G · 1234 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 1230 Å² buried · 16 hydrogen bonds · protein-protein
B–H · 906 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 covalent (covalent ligand).

Compared structures

7RRJ · Crystal structure of fast switching M159Q mutant of fluorescent protein Dronpa (Dronpa2) · the same entry in another collection · chain G against G, 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 7RRJ · PDBe 7RRJ · UniProt Q5TLG6

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