MolNFT v1 · #164217 · protein

Crystal structure of human SHIP2 catalytic domain in complex with 1,2, 4 dimer

6SQU · Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2: “Crystal structure of human SHIP2 catalytic domain in complex with 1,2, 4 dimer”. X-ray diffraction, 1 ligand (D7I), 6 pockets (best druggability 0.54). MolNFT v1 #164217 on…

PDB: 6SQU
Type: protein
Length: 580 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
EC: 3.1.3.86
UniProt: O15357
Ligands: D7I
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86)	protein	274	23% helix, 35% strand	O15357
B	Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86)	protein	306	22% helix, 34% strand	O15357

Ligands and binding sites

D7I · 5,5'-(ethane-1,2-diylbis(oxy))bis(benzene-5,4,2,1,-tetrayl)hexakisphosphate · ligand · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	56	0.54	0.88	17	empty
2	293	0.51	0.74	39	empty
3	64	0.50	0.85	18	empty
4	150	0.43	0.75	22	empty
5	61	0.37	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 527 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6SQU · Crystal structure of human SHIP2 catalytic domain in complex with 1,2,4 Dimer · the same entry in another collection · chain A against A, TM-score 1.00
O15357 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3,4,5-trisphosphate… · a predicted model of the same protein · chain A 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 O15357
Elsewhere: RCSB PDB 6SQU · PDBe 6SQU · UniProt O15357

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