MolNFT v1 · #56177 · protein

Crystal structure of a photoswitchable GFP-like protein dronpa in the bright-state

2Z6Z · Fluorescent protein dronpa: “Crystal structure of a photoswitchable GFP-like protein dronpa in the bright-state”. X-ray diffraction, 1 ligand (GYC), 14 pockets (best druggability 0.84). MolNFT v1 #56177 on GenesisL1: 3D structure…

PDB: 2Z6Z
Type: protein
Length: 1,292 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein dronpa
UniProt: Q5TLG6
Ligands: GYC
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 4% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Fluorescent protein dronpa	protein	216	6% helix, 57% strand	Q5TLG6
B	Fluorescent protein dronpa	protein	215	4% helix, 58% strand	Q5TLG6
C	Fluorescent protein dronpa	protein	217	4% helix, 57% strand	Q5TLG6
D	Fluorescent protein dronpa	protein	213	4% helix, 58% strand	Q5TLG6
F	Fluorescent protein dronpa	protein	215	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 · 6 copies · chains A, B, C, D, E, F

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1021	0.84	0.85	114	empty
2	80	0.76	0.99	26	GYC
3	75	0.75	0.99	27	GYC
4	84	0.75	0.98	27	GYC
5	73	0.74	0.98	24	GYC

Interfaces

8 interfaces between chains.

A–C · 1234 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1069 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 868 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 864 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 856 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 covalent (covalent ligand).

Compared structures

2Z6Z · Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state · the same entry in another collection · chain B against B, 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 2Z6Z · PDBe 2Z6Z · UniProt Q5TLG6

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