MolNFT v1 · #126689 · protein

GFP-binding darpin 3G61

5MAD: “GFP-binding darpin 3G61”. X-ray diffraction, 2 ligands (CRO, NA), 19 pockets (best druggability 0.80). MolNFT v1 #126689 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MAD
Type: protein
Length: 1,544 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3G61; Green fluorescent protein
UniProt: P42212
Ligands: CRO, NA
Pockets: 19 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 28% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3G61	protein	154	52% helix, 0% strand	—
B, D	Green fluorescent protein	protein	231	11% helix, 51% strand	P42212
C	3G61	protein	155	52% helix, 0% strand	—
E, G	3G61	protein	160	53% helix, 0% strand	—
F	Green fluorescent protein	protein	225	11% helix, 52% strand	P42212
H	Green fluorescent protein	protein	228	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 · 4 copies · chains B, D, F, H
NA · Sodium ion · metal · chains E, H
PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1071	0.80	0.81	90	PEG
2	105	0.78	0.97	26	CRO
3	99	0.78	0.98	26	CRO
4	97	0.77	0.98	26	CRO
5	1129	0.77	0.79	91	empty

Interfaces

12 interfaces between chains.

C–D · 871 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 829 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 824 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 816 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 526 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

5MAD · GFP-binding DARPin 3G61 · the same entry in another collection · chain H against H, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain F 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 5MAD · PDBe 5MAD · UniProt P42212

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