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Ca-like domain of mouse ptprg

Analyse Ca-like domain of mouse ptprg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JXG
Type: protein
Length: 1,039 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor-type tyrosine-protein phosphatase gamma
EC: 3.1.3.48
UniProt: Q05909
Pockets: 15 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor-type tyrosine-protein phosphatase gamma (EC 3.1.3.48)	protein	257	18% helix, 30% strand	Q05909
B	Receptor-type tyrosine-protein phosphatase gamma (EC 3.1.3.48)	protein	259	18% helix, 31% strand	Q05909
C	Receptor-type tyrosine-protein phosphatase gamma (EC 3.1.3.48)	protein	264	17% helix, 32% strand	Q05909
D	Receptor-type tyrosine-protein phosphatase gamma (EC 3.1.3.48)	protein	259	18% helix, 32% strand	Q05909

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	441	0.72	0.82	65	empty
2	172	0.64	0.85	27	empty
3	232	0.53	0.76	28	empty
4	110	0.50	0.81	22	empty
5	175	0.49	0.76	24	empty

Interfaces

5 interfaces between chains.

B–D · 732 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 337 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 285 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 238 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 110 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3JXG · CA-like domain of mouse PTPRG · the same entry in another collection · chain D against D, TM-score 1.00
Q05909 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase gamma… · 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 Q05909
Elsewhere: RCSB PDB 3JXG · PDBe 3JXG · UniProt Q05909

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