Research workbench

GFP-binding darpin fusion GC_R7

Analyse GFP-binding darpin fusion GC_R7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MAK
Type: protein
Length: 1,025 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein; R7
UniProt: P42212
Ligands: CRO
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Green fluorescent protein	protein	227	11% helix, 51% strand	P42212
A, C	R7	protein	286	51% helix, 0% strand	—
D	Green fluorescent protein	protein	226	11% 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 · 2 copies · chains B, D
CIT · Citric acid · additive · 5 copies · chains A, C

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.78	0.99	26	CRO
2	91	0.78	0.98	25	CRO
3	451	0.68	0.80	49	empty
4	406	0.68	0.80	52	empty
5	53	0.63	0.94	22	empty

Interfaces

3 interfaces between chains.

B–A · 1854 Å² buried · 16 hydrogen bonds · protein-protein
D–C · 1808 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 128 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

5MAK · GFP-binding DARPin fusion gc_R7 · 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 D 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 5MAK · PDBe 5MAK · UniProt P42212

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