MolNFT v1 · #158327 · protein

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

6NQJ: “Crystal structure of fast switching M159T mutant of fluorescent protein dronpa (DRONPA2)”. X-ray diffraction, 1 ligand (GYC), 14 pockets (best druggability 0.82). MolNFT v1 #158327 on GenesisL1: 3D structure, binding sites and…

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

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