MolNFT v1 · #103392 · protein

Crystal structure of vsfgfp-0

4PFE · Green fluorescent protein: “Crystal structure of vsfgfp-0”. X-ray diffraction, 1 ligand (CRO), 5 pockets (best druggability 0.77). MolNFT v1 #103392 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PFE
Type: protein
Length: 682 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CRO
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	342	7% helix, 52% strand	P42212
B	Green fluorescent protein	protein	340	9% helix, 52% strand	P42212

Ligands and binding sites

CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.77	0.98	25	CRO
2	85	0.77	0.98	25	CRO
3	596	0.63	0.74	67	empty
4	250	0.51	0.75	32	empty
5	183	0.46	0.75	31	empty

Interfaces

1 interface between chains.

A–B · 1424 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

4PFE · Crystal structure of vsfGFP-0 · 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 0.67

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 4PFE · PDBe 4PFE · UniProt P42212

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.