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Structure of human laforin dual specificity phosphatase domain

Analyse Structure of human laforin dual specificity phosphatase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R30
Type: protein
Length: 716 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Laforin
EC: 3.1.3.-, 3.1.3.16, 3.1.3.48
UniProt: O95278
Ligands: SO4
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Laforin (EC 3.1.3.-, 3.1.3.16, 3.1.3.48)	protein	179	49% helix, 12% strand	O95278

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
BME · Beta-mercaptoethanol · additive · 12 copies · chains A, C, B, D

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

Pockets

9 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	943	0.72	0.76	80	BME
2	525	0.65	0.77	61	BME
3	227	0.58	0.79	38	empty
4	164	0.50	0.78	22	empty
5	51	0.49	0.87	20	BME

Interfaces

4 interfaces between chains.

B–D · 1147 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 689 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 392 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 covalent (additive adduct).

Compared structures

4R30 · Structure of human laforin dual specificity phosphatase domain · the same entry in another collection · chain D against D, TM-score 1.00
O95278 · AlphaFold monomer V2.0 prediction for laforin (O95278) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 O95278
Elsewhere: RCSB PDB 4R30 · PDBe 4R30 · UniProt O95278

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