MolNFT v1 · #82903 · protein

Structure of a pressure sensitive YFP variant YFP-G3

3W1D · Green fluorescent protein: “Structure of a pressure sensitive YFP variant YFP-G3”. X-ray diffraction, 1 ligand (CR2), 2 pockets (best druggability 0.68). MolNFT v1 #82903 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3W1D
Type: protein
Length: 226 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CR2
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	226	12% helix, 52% strand	P42212

Ligands and binding sites

CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	153	0.68	0.88	28	CR2
2	55	0.35	0.78	13	empty

Modifications

Observed in the structure: 2 cofactor (chromophore).

Compared structures

3W1D · Structure of a pressure sensitive YFP variant YFP-G3 · the same entry in another collection · chain A against A, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P42212
Elsewhere: RCSB PDB 3W1D · PDBe 3W1D · UniProt P42212

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