MolNFT v1 · #5581 · protein

Green fluorescent protein from aequorea victoria, mutant

1EMC: “Green fluorescent protein from aequorea victoria, mutant”. X-ray diffraction, 1 ligand (GYS), 10 pockets (best druggability 0.77). MolNFT v1 #5581 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1EMC
Type: protein
Length: 897 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: GYS
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Green fluorescent protein	protein	224	10% helix, 53% strand	P42212
C	Green fluorescent protein	protein	225	7% helix, 52% 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 · 4 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.77	0.97	26	GYS
2	97	0.76	0.97	27	GYS
3	103	0.76	0.97	27	GYS
4	95	0.76	0.97	24	GYS
5	805	0.74	0.79	73	empty

Interfaces

5 interfaces between chains.

C–D · 393 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 379 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 258 Å² buried · 1 hydrogen bond · protein-protein
A–C · 166 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 50 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

1EMC · Green fluorescent protein from aequorea victoria, mutant · the same entry in another collection · chain D against D, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain D 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 P42212
Elsewhere: RCSB PDB 1EMC · PDBe 1EMC · UniProt P42212

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