MolNFT v1 · #153588 · protein

Crystal structure of OSHXK6-ATP-MG2+ complex

6JJ8 · Rice hexokinase 6: “Crystal structure of OSHXK6-ATP-MG2+ complex”. X-ray diffraction, 3 ligands (ADP, MG, PO4), 17 pockets (best druggability 0.77). MolNFT v1 #153588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JJ8
Type: protein
Length: 1,395 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rice hexokinase 6
EC: 2.7.1.1
UniProt: Q8LQ68
Ligands: ADP, MG, PO4
Pockets: 17 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A, B	Rice hexokinase 6 (EC 2.7.1.1)	protein	465	44% helix, 19% strand	Q8LQ68

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C, A, B
MG · Magnesium ion · metal · 3 copies · chains C, A, B
PO4 · Phosphate ion · ion · 3 copies · chains C, A, B

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

Pockets

17 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	876	0.77	0.81	97	ADP, PO4, MG
2	753	0.71	0.77	69	empty
3	694	0.70	0.77	64	empty
4	519	0.68	0.79	69	ADP, PO4, MG
5	487	0.65	0.77	47	ADP, PO4, MG

Interfaces

3 interfaces between chains.

C–B · 654 Å² buried · 5 hydrogen bonds · protein-protein
C–A · 647 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 640 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6JJ8 · Crystal structure of OsHXK6-ATP-Mg2+ complex · the same entry in another collection · chain C against C, TM-score 1.00
Q8LQ68 · AlphaFold monomer V2.0 prediction for hexokinase-6 (Q8LQ68) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q8LQ68
Elsewhere: RCSB PDB 6JJ8 · PDBe 6JJ8 · UniProt Q8LQ68

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