MolNFT v1 · #186737 · protein

NSH2 domain of P85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53

7RNU · Phosphatidylinositol 3-kinase regulatory subunit beta: “NSH2 domain of P85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with…”. X-ray diffraction, 4 pockets (best druggability 0.70). MolNFT v1…

PDB: 7RNU
Type: protein
Length: 461 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphatidylinositol 3-kinase regulatory subunit beta; Actin, alpha skeletal muscle
UniProt: O00459, P68133
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 8 distinct chains · 18% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphatidylinositol 3-kinase regulatory subunit beta	protein	107	18% helix, 28% strand	O00459
B	Actin, alpha skeletal muscle	protein	5	0% helix, 20% strand	P68133
C	Phosphatidylinositol 3-kinase regulatory subunit beta	protein	110	19% helix, 27% strand	O00459
D	Actin, alpha skeletal muscle	protein	9	0% helix, 33% strand	P68133
E	Phosphatidylinositol 3-kinase regulatory subunit beta	protein	106	20% helix, 29% strand	O00459
F	Actin, alpha skeletal muscle	protein	8	0% helix, 25% strand	P68133
G	Phosphatidylinositol 3-kinase regulatory subunit beta	protein	109	19% helix, 29% strand	O00459
H	Actin, alpha skeletal muscle	protein	7	0% helix, 29% strand	P68133

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, D, E, F, G

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	814	0.70	0.76	62	EDO
2	263	0.60	0.80	43	EDO
3	87	0.45	0.81	18	empty
4	58	0.33	0.77	14	empty

Interfaces

14 interfaces between chains.

E–G · 728 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 640 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 601 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 492 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 480 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

7RNU · nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin… · the same entry in another collection · chain H against H, TM-score 1.00
O00459 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase regulatory subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O00459
Every structure of UniProt P68133
Elsewhere: RCSB PDB 7RNU · PDBe 7RNU · UniProt O00459 · UniProt P68133

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