MolNFT v1 · #145959 · protein

Photodissociable dimeric dronpa green fluorescent protein variant M (pddronpam)

6D38 · Fluorescent protein dronpa: “Photodissociable dimeric dronpa green fluorescent protein variant M (pddronpam)”. X-ray diffraction, 2 ligands (GYC, SO4), 1 pocket (best druggability 0.78). MolNFT v1 #145959 on GenesisL1: 3D structure…

PDB: 6D38
Type: protein
Length: 212 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein dronpa
UniProt: Q5TLG6
Ligands: GYC, SO4
Pockets: 1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein dronpa	protein	212	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 · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	92	0.78	0.99	31	GYC

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

6D38 · Photodissociable dimeric Dronpa green fluorescent protein variant M (pdDronpaM) · 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 6D38 · PDBe 6D38 · UniProt Q5TLG6

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