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Crystal structure of PTPN22 in complex with skap-hom PTYR75 peptide

Analyse Crystal structure of PTPN22 in complex with skap-hom PTYR75 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OMH
Type: protein
Length: 1,208 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein phosphatase non-receptor type 22; Src kinase-associated phosphoprotein 2
EC: 3.1.3.48
UniProt: Q9Y2R2, O75563
Pockets: 18 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Tyrosine-protein phosphatase non-receptor type 22 (EC 3.1.3.48)	protein	294	35% helix, 17% strand	Q9Y2R2
B	Tyrosine-protein phosphatase non-receptor type 22 (EC 3.1.3.48)	protein	291	39% helix, 21% strand	Q9Y2R2
E, F, G	Src kinase-associated phosphoprotein 2	protein	9	0% helix, 0% strand	O75563
H	Src kinase-associated phosphoprotein 2	protein	8	0% helix, 0% strand	O75563

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	721	0.76	0.81	60	empty
2	815	0.72	0.77	89	empty
3	308	0.59	0.78	47	empty
4	380	0.59	0.76	49	empty
5	272	0.55	0.76	26	empty

Interfaces

9 interfaces between chains.

A–E · 599 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 575 Å² buried · 1 hydrogen bond · protein-protein
C–G · 552 Å² buried · 16 hydrogen bonds · protein-protein
B–F · 528 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 496 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

3OMH · Crystal structure of PTPN22 in complex with SKAP-HOM pTyr75 peptide · the same entry in another collection · chain H against H, TM-score 1.00
Q9Y2R2 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 22… · a predicted model of the same protein · chain B against A, TM-score 0.97
O75563 · AlphaFold monomer V2.0 prediction for src kinase-associated phosphoprotein 2 (O75563) · a predicted model of the same protein · chain H against A, TM-score 0.45

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 Q9Y2R2
Every structure of UniProt O75563
Elsewhere: RCSB PDB 3OMH · PDBe 3OMH · UniProt Q9Y2R2 · UniProt O75563

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