MolNFT v1 · #110408 · protein

X-ray structure of bgfp-C / egfp complex

4XVP · Green fluorescent protein: “X-ray structure of bgfp-C / egfp complex”. X-ray diffraction, 1 ligand (CRO), 9 pockets (best druggability 0.79). MolNFT v1 #110408 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XVP
Type: protein
Length: 1,155 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein; Bgfp-C
UniProt: P42212
Ligands: CRO
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Green fluorescent protein	protein	227	8% helix, 50% strand	P42212
D, E, F	Bgfp-C	protein	158	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 · 3 copies · chains A, B, C

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

Pockets

9 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	914	0.79	0.82	93	empty
2	96	0.78	0.98	25	CRO
3	92	0.77	0.98	25	CRO
4	96	0.77	0.97	25	CRO
5	961	0.76	0.79	97	empty

Interfaces

8 interfaces between chains.

A–D · 1406 Å² buried · 25 hydrogen bonds · protein-protein
B–E · 1393 Å² buried · 24 hydrogen bonds · protein-protein
C–F · 1362 Å² buried · 26 hydrogen bonds · protein-protein
A–E · 538 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 469 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor (chromophore).

Compared structures

4XVP · X-ray structure of bGFP-C / EGFP complex · the same entry in another collection · chain F against F, 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 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 4XVP · PDBe 4XVP · UniProt P42212

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