Research workbench

Human GKRP bound to AMG-5980 and S6P

Analyse Human GKRP bound to AMG-5980 and S6P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MRO
Type: protein
Length: 1,175 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Homo sapiens
Molecule: Glucokinase regulatory protein
UniProt: Q14397
Ligands: MG0, S6P, IOD, SO4
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · resolution 2.2 · 2 distinct chains · 52% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucokinase regulatory protein	protein	585	52% helix, 11% strand	Q14397
B	Glucokinase regulatory protein	protein	590	53% helix, 11% strand	Q14397

Ligands and binding sites

MG0 · 2-(4-{4-[(6-aminopyridin-3-yl)sulfonyl]piperazin-1-yl}phenyl)-1,1,1,3,3,3-hexafluoropropan-2-ol · ligand · 2 copies · chains A, B
S6P · D-sorbitol-6-phosphate · sugar · 2 copies · chains A, B
IOD · Iodide ion · ion · 25 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains B
GOL · Glycerol · additive · chains A

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

Pockets

14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.83	0.89	59	MG0, S6P, IOD
2	564	0.83	0.89	61	MG0, S6P, IOD
3	770	0.74	0.79	99	IOD
4	190	0.57	0.80	43	IOD
5	106	0.55	0.84	24	IOD

Interfaces

1 interface between chains.

A–B · 669 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4MRO · Human gkrp bound to amg-5980 and S6P · the same entry in another collection · chain A against A, TM-score 1.00
Q14397 · AlphaFold monomer V2.0 prediction for glucokinase regulatory protein (Q14397) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q14397
Elsewhere: RCSB PDB 4MRO · PDBe 4MRO · UniProt Q14397

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.