MolNFT v1 · #110061 · protein

X-ray structure of bgfp-a / egfp complex

4XL5 · Green fluorescent protein: “X-ray structure of bgfp-a / egfp complex”. X-ray diffraction, 1 ligand (CRO), 5 pockets (best druggability 0.79). MolNFT v1 #110061 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XL5
Type: protein
Length: 471 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein; Bgfp-a
UniProt: P42212
Ligands: CRO
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	226	10% helix, 51% strand	P42212
C	Bgfp-a	protein	245	77% helix, 0% strand	—

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 · chains A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.79	0.98	24	CRO
2	827	0.78	0.81	85	empty
3	177	0.53	0.79	27	empty
4	78	0.39	0.78	17	empty
5	59	0.34	0.77	16	empty

Interfaces

1 interface between chains.

A–C · 1028 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (chromophore).

Compared structures

4XL5 · X-ray structure of bGFP-A / EGFP complex · 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 4XL5 · PDBe 4XL5 · UniProt P42212

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