MolNFT v1 · #64969 · protein

Photoactivated state of pa-GFP

3GJ2 · Green fluorescent protein: “Photoactivated state of pa-GFP”. X-ray diffraction, 2 ligands (CRO, CL), 18 pockets (best druggability 0.78). MolNFT v1 #64969 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3GJ2
Type: protein
Length: 903 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CRO, CL
Pockets: 18 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	226	11% helix, 52% strand	P42212
B	Green fluorescent protein	protein	228	10% helix, 52% strand	P42212
C	Green fluorescent protein	protein	224	9% helix, 53% strand	P42212
D	Green fluorescent protein	protein	225	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 · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 3 copies · chains A, B, C, D

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

Pockets

18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.78	0.99	25	CRO
2	93	0.77	0.98	23	CRO
3	78	0.76	0.99	22	CRO
4	86	0.76	0.98	21	CRO
5	776	0.75	0.80	92	CL

Interfaces

5 interfaces between chains.

A–B · 1016 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1007 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 634 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 118 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 12 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

3GJ2 · Photoactivated state of PA-GFP · 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 C 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 3GJ2 · PDBe 3GJ2 · UniProt P42212

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