MolNFT v1 · #121579 · protein

GFP mutant S205G

5HZO · Green fluorescent protein: “GFP mutant S205G”. X-ray diffraction, 3 ligands (GYS, MLT, UMQ), 5 pockets (best druggability 0.80). MolNFT v1 #121579 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HZO
Type: protein
Length: 458 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: GYS, MLT, UMQ
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	229	7% helix, 51% strand	P42212
B	Green fluorescent protein	protein	229	10% helix, 51% strand	P42212

Ligands and binding sites

GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
MLT · D-malate · ligand · 2 copies · chains A, B
UMQ · Undecyl-maltoside · ligand · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	151	0.80	0.97	32	GYS, MLT
2	143	0.80	0.97	35	GYS, MLT
3	102	0.49	0.81	29	empty
4	199	0.46	0.74	36	UMQ
5	79	0.41	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 281 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

5HZO · GFP mutant S205G · 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 B 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 5HZO · PDBe 5HZO · UniProt P42212

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