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Human gkrp bound to AMG2882 and sorbitol-6-phosphate

Analyse Human gkrp bound to AMG2882 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: 4PX2
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: 2WY, S6P, IOD, SO4
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucokinase regulatory protein	protein	585	54% helix, 11% strand	Q14397
B	Glucokinase regulatory protein	protein	590	54% helix, 11% strand	Q14397

Ligands and binding sites

2WY · N-[(R)-1-benzofuran-2-yl(phenyl)methyl]-3,4-dihydro-2H-1,5-benzodioxepine-7-sulfonamide · ligand · 2 copies · chains A, B
S6P · D-sorbitol-6-phosphate · ligand · 2 copies · chains A, B
IOD · Iodide ion · ion · 28 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	495	0.84	0.91	56	2WY, S6P
2	522	0.84	0.90	60	2WY, S6P, IOD
3	822	0.72	0.77	96	IOD
4	116	0.54	0.83	22	IOD
5	93	0.53	0.84	20	IOD

Interfaces

1 interface between chains.

A–B · 679 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4PX2 · Human GKRP bound to AMG2882 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 4PX2 · PDBe 4PX2 · UniProt Q14397

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