MolNFT v1 · #48300 · protein

Dark state structure of the reversibly switchable fluorescent protein dronpa

2POX: “Dark state structure of the reversibly switchable fluorescent protein dronpa”. X-ray diffraction, 1 ligand (GYC), 10 pockets (best druggability 0.86). MolNFT v1 #48300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2POX
Type: protein
Length: 866 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein dronpa
UniProt: Q5TLG6
Ligands: GYC
Pockets: 10 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein dronpa	protein	218	6% helix, 57% strand	Q5TLG6
B	Fluorescent protein dronpa	protein	219	5% helix, 57% strand	Q5TLG6
C	Fluorescent protein dronpa	protein	215	6% helix, 58% strand	Q5TLG6
D	Fluorescent protein dronpa	protein	214	6% 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

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1000	0.86	0.87	129	empty
2	86	0.77	0.99	24	GYC
3	90	0.77	0.98	24	GYC
4	72	0.74	0.98	24	GYC
5	66	0.72	0.98	21	GYC

Interfaces

6 interfaces between chains.

C–D · 919 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 908 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 568 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 407 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 400 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2POX · Dark state structure of the reversibly switchable fluorescent protein Dronpa · 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 2POX · PDBe 2POX · UniProt Q5TLG6

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