Research workbench

Human gkrp bound to amg-5112 and sorbitol-6-phosphate

Analyse Human gkrp bound to amg-5112 and sorbitol-6-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OP3
Type: protein
Length: 1,175 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucokinase regulatory protein
UniProt: Q14397
Ligands: 2UY, S6P, IOD, SO4
Pockets: 13 · best druggability 0.84

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucokinase regulatory protein	protein	585	51% helix, 11% strand	Q14397
B	Glucokinase regulatory protein	protein	590	53% helix, 11% strand	Q14397

Ligands and binding sites

2UY · (2S)-2-{6'-[(6-aminopyridin-3-yl)sulfonyl]-2'-(phenylamino)-2,3'-bipyridin-5-yl}-1,1,1-trifluoropropan-2-ol · ligand · 2 copies · chains A, B
S6P · D-sorbitol-6-phosphate · ligand · 2 copies · chains A, B
IOD · Iodide ion · ion · 25 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains B
GOL · Glycerol · additive · 2 copies · chains B

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

Pockets

13 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	538	0.84	0.90	59	2UY, S6P, IOD
2	549	0.83	0.89	67	2UY, S6P, IOD
3	865	0.76	0.79	101	IOD
4	154	0.56	0.82	35	IOD, GOL
5	105	0.56	0.85	26	IOD

Interfaces

1 interface between chains.

A–B · 673 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4OP3 · Human GKRP bound to AMG-5112 and Sorbitol-6-phosphate · 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 4OP3 · PDBe 4OP3 · UniProt Q14397

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