Research workbench

GFP-40/GFPUV complex, form I

Analyse GFP-40/GFPUV complex, form I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CD7
Type: protein
Length: 668 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein; GFP-40
UniProt: P42212
Ligands: CRO
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	Green fluorescent protein	protein	235	13% helix, 50% strand	P42212
A, C	GFP-40	protein	99	17% helix, 47% 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 · 2 copies · chains B, D

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	84	0.76	0.98	26	CRO
2	95	0.75	0.96	25	CRO
3	129	0.43	0.76	19	empty
4	113	0.42	0.77	20	empty
5	63	0.30	0.74	12	empty

Interfaces

4 interfaces between chains.

B–A · 669 Å² buried · 10 hydrogen bonds · protein-protein
D–C · 661 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 182 Å² buried · 4 hydrogen bonds · protein-protein
D–A · 53 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

7CD7 · GFP-40/GFPuv complex, Form I · the same entry in another collection · chain B against B, 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 0.98

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 7CD7 · PDBe 7CD7 · UniProt P42212

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