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GFP-binding darpin fusion GC_R11

Analyse GFP-binding darpin fusion GC_R11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MA9
Type: protein
Length: 2,083 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein; R11
UniProt: P42212
Ligands: CRO
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D, H, F	Green fluorescent protein	protein	226	11% helix, 52% strand	P42212
A	R11	protein	298	50% helix, 0% strand	—
C, G	R11	protein	294	51% helix, 0% strand	—
E	R11	protein	293	51% 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 · 4 copies · chains B, D, H, F
EDO · 1,2-ethanediol · additive · 11 copies · chains B, A, F, C, H, D, G, E

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	109	0.79	0.98	28	CRO
2	1002	0.78	0.80	77	EDO
3	101	0.78	0.98	25	CRO
4	103	0.78	0.98	25	CRO
5	927	0.77	0.80	74	empty

Interfaces

13 interfaces between chains.

C–D · 1789 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1759 Å² buried · 13 hydrogen bonds · protein-protein
B–A · 1735 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1719 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 317 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

5MA9 · GFP-binding DARPin fusion gc_R11 · 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 D 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 5MA9 · PDBe 5MA9 · UniProt P42212

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