MolNFT v1 · #139225 · protein

Crystal structure of SHP2_SH2-caga EPIYA_D peptide complex

5X94 · Tyrosine-protein phosphatase non-receptor type 11: “Crystal structure of SHP2_SH2-caga EPIYA_D peptide complex”. X-ray diffraction, 2 pockets (best druggability 0.47). MolNFT v1 #139225 on GenesisL1: 3D structure, binding sites and…

PDB: 5X94
Type: protein
Length: 449 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein phosphatase non-receptor type 11; Cag pathogenicity island protein
EC: 3.1.3.48
UniProt: Q06124, E6NP29
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 6 distinct chains · 18% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48)	protein	206	19% helix, 32% strand	Q06124
B	Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48)	protein	207	19% helix, 30% strand	Q06124
L	Cag pathogenicity island protein	protein	9	0% helix, 33% strand	E6NP29
M	Cag pathogenicity island protein	protein	7	0% helix, 29% strand	E6NP29
N	Cag pathogenicity island protein	protein	13	0% helix, 15% strand	E6NP29
O	Cag pathogenicity island protein	protein	7	0% helix, 14% strand	E6NP29

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.47	0.76	25	empty
2	167	0.46	0.75	29	empty

Interfaces

5 interfaces between chains.

A–N · 664 Å² buried · 10 hydrogen bonds · protein-protein
A–L · 591 Å² buried · 10 hydrogen bonds · protein-protein
B–M · 556 Å² buried · 10 hydrogen bonds · protein-protein
B–O · 495 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 194 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered, phosphorylation).

Compared structures

5X94 · Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex · the same entry in another collection · chain A against A, TM-score 1.00

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 Q06124
Every structure of UniProt E6NP29
Elsewhere: RCSB PDB 5X94 · PDBe 5X94 · UniProt Q06124 · UniProt E6NP29

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