MolNFT v1 · #126680 · protein

GFP-binding darpin fusion GC_K7

5MA4 · Green fluorescent protein: “GFP-binding darpin fusion GC_K7”. X-ray diffraction, 1 ligand (CRO), 4 pockets (best druggability 0.78). MolNFT v1 #126680 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MA4
Type: protein
Length: 523 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein; K7
UniProt: P42212
Ligands: CRO
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Green fluorescent protein	protein	229	11% helix, 51% strand	P42212
A	K7	protein	294	50% 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 B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.78	0.98	25	CRO
2	492	0.71	0.81	62	empty
3	360	0.67	0.80	40	empty
4	249	0.59	0.79	35	empty

Interfaces

1 interface between chains.

B–A · 1736 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (chromophore).

Compared structures

5MA4 · GFP-binding DARPin fusion gc_K7 · 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 0.99

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 5MA4 · PDBe 5MA4 · UniProt P42212

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