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GFP-binding darpin 3G124NC

Analyse GFP-binding darpin 3G124NC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MA8
Type: protein
Length: 764 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ga-binding protein subunit beta-1; Green fluorescent protein
UniProt: P42212
Ligands: CRO
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ga-binding protein subunit beta-1	protein	157	55% helix, 0% strand	—
C	Ga-binding protein subunit beta-1	protein	158	56% helix, 0% strand	—
B	Green fluorescent protein	protein	225	11% helix, 52% strand	P42212
D	Green fluorescent protein	protein	224	10% 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

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	105	0.79	0.98	27	CRO
2	105	0.77	0.97	27	CRO
3	219	0.60	0.81	39	empty
4	122	0.59	0.85	24	empty
5	241	0.59	0.80	40	empty

Interfaces

4 interfaces between chains.

A–B · 935 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 919 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 148 Å² buried · 0 hydrogen bonds · protein-protein
C–B · 18 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

5MA8 · GFP-binding DARPin 3G124nc · the same entry in another collection · chain A against A, 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 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 5MA8 · PDBe 5MA8 · UniProt P42212

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