MolNFT v1 · #127293 · protein

GFP nuclear transport receptor mimic 3B8

5MSE · Green fluorescent protein: “GFP nuclear transport receptor mimic 3B8”. X-ray diffraction, 2 ligands (CRO, NA), 19 pockets (best druggability 0.80). MolNFT v1 #127293 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MSE
Type: protein
Length: 895 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CRO, NA
Pockets: 19 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, B	Green fluorescent protein	protein	223	11% helix, 52% strand	P42212
C	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 · 4 copies · chains A, C, D, B
NA · Sodium ion · metal · 8 copies · chains A, C, D, B
IMD · Imidazole · additive · 4 copies · chains A, D, C, B

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

Pockets

19 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	976	0.80	0.82	136	IMD
2	99	0.77	0.98	28	CRO
3	99	0.77	0.97	26	CRO
4	98	0.77	0.97	26	CRO
5	95	0.76	0.97	27	CRO

Interfaces

4 interfaces between chains.

A–C · 812 Å² buried · 6 hydrogen bonds · protein-protein
D–B · 792 Å² buried · 5 hydrogen bonds · protein-protein
C–B · 788 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 777 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

5MSE · GFP nuclear transport receptor mimic 3B8 · 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 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 5MSE · PDBe 5MSE · UniProt P42212

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