Research workbench

Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation

Analyse Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4I5L
Type: protein
Length: 2,481 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.43
Source: Homo sapiens; Microcystis aeruginosa
Molecule: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform…
EC: 3.1.3.16
UniProt: P30153, Q9Y5P8, Q99741, P67775
Ligands: CA, MN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.43 · 5 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	protein	582	79% helix, 0% strand	P30153
B	Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct	protein	356	62% helix, 6% strand	Q9Y5P8, Q99741
C, F	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha (EC 3.1.3.16)	protein	295	37% helix, 18% strand	P67775
E	Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct	protein	357	62% helix, 5% strand	Q9Y5P8, Q99741
G, H	Microcystin-LR (MCLR) bound form	protein	7	0% helix, 0% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains B, E
MN · Manganese (II) ion · metal · 4 copies · chains C, F, G
PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, F, B, C, D, E
MLI · Malonate ion · additive · 3 copies · chains C, E, F

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	989	0.81	0.82	95	PEG
2	897	0.75	0.78	83	empty
3	886	0.72	0.77	70	empty
4	304	0.56	0.76	33	empty
5	289	0.55	0.76	38	PEG, MLI

Interfaces

10 interfaces between chains.

D–E · 1700 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1680 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1100 Å² buried · 25 hydrogen bonds · protein-protein
D–F · 1071 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 712 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 2 d-amino (nonstandard, D-amino acid).

Compared structures

4I5L · Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for CDC6… · the same entry in another collection · chain B against B, TM-score 1.00
P67775 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A catalytic… · a predicted model of the same protein · chain C against A, TM-score 0.99
P30153 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A 65 kda… · a predicted model of the same protein · chain A against A, TM-score 0.99
Q9Y5P8 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A regulatory… · a predicted model of the same protein · chain E 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 P30153
Every structure of UniProt Q9Y5P8
Every structure of UniProt Q99741
Every structure of UniProt P67775
Elsewhere: RCSB PDB 4I5L · PDBe 4I5L · UniProt P30153 · UniProt Q9Y5P8 · UniProt Q99741 · UniProt P67775

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