5X94: SHP2_SH2-CagA EPIYA_D peptide complex

Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 13 Sept 2017.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Helicobacter pylori
Chains: 6
Atoms: 3,546
Mol. weight: 56.09 kDa
Released: 13 Sept 2017

Explore 5X94 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X94 contains 11 α-helices and 49 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
α-helix	13-22	10
β-strand	28-33	6	1
β-strand	41-47	7	1
β-strand	50-56	7	1
β-strand	57-58	2	2
β-strand	63-64	2	2
β-strand	71	1	2
α-helix	74-83	10
β-strand	89	1	3
β-strand	90	1	4
β-strand	95	1	3
β-strand	100-101	2	1
β-strand	113-115	3	5
α-helix	119-128	10
β-strand	134-139	6	5
β-strand	147-153	7	5
β-strand	166-172	7	5
β-strand	173-174	2	6
β-strand	179-180	2	6
β-strand	187	1	6
α-helix	190-199	10
β-strand	202-203	2	7
β-strand	204	1	8
β-strand	209-210	2	7
β-strand	214-215	2	5

Chain B: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	9
α-helix	13-22	10
β-strand	28-33	6	9
β-strand	41-47	7	9
β-strand	50-56	7	9
β-strand	57-58	2	10
β-strand	63-64	2	10
β-strand	71	1	10
α-helix	74-82	9
β-strand	90	1	11
β-strand	100-101	2	9
β-strand	113-115	3	12
α-helix	119-128	10
β-strand	135-139	5	12
β-strand	147-152	6	12
β-strand	167-172	6	12
β-strand	173-175	3	13
β-strand	178-180	3	13
β-strand	187	1	13
α-helix	190-199	10
β-strand	202-203	2	14
β-strand	204	1	15
β-strand	209-210	2	14
β-strand	215	1	12

Chain L: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	955-956	2	1
α-helix	957-958	2
β-strand	959	1	4
α-helix	960	1

Chain M: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	956	1	9
β-strand	959	1	11

Chain N: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	952-954	3
β-strand	956	1	5
β-strand	959	1	8

Chain O: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	959	1	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein phosphatase non-receptor type 11	A, B	protein	220	Homo sapiens	Q06124 (AlphaFold model)
Cag pathogenicity island protein	L, M, N, O	protein	13	Helicobacter pylori	P55980 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5X94_1 Tyrosine-protein phosphatase non-receptor type 11 (chains A, B)
MTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTG
DYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGK
EAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYD
VGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTR

Sequence of entity 2 (L, M, N, O), FASTA

>5X94_2 Cag pathogenicity island protein (chains L, M, N, O)
ASPEPIYATIDFD

Primary citation

Differential Mechanisms for SHP2 Binding and Activation Are Exploited by Geographically Distinct Helicobacter pylori CagA Oncoproteins. Hayashi, T., Senda, M., Suzuki, N. et al. Cell Rep (2017) 20:2876-2890. DOI 10.1016/j.celrep.2017.08.080 · PubMed

Other PDB entries of the same protein (UniProt Q06124 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EIK 1.25 Å, Crystal structure of N-SH2 domain of SHP2 with T42A mutation bound to GAB1 tyrosine…
3ZM1 1.4 Å, Catalytic domain of human SHP2
4JMG 1.4 Å, Crystal structure of the synthetic protein in complex with pY peptide
7PPM 1.48 Å, SHP2 catalytic domain in complex with IRS1 (889-901) phosphopeptide (pSer-892, pTyr-896)
3ZM0 1.5 Å, Catalytic domain of human SHP2
3ZM2 1.5 Å, Catalytic domain of human SHP2
3ZM3 1.5 Å, Catalytic domain of human SHP2
7PPL 1.53 Å, SHP2 catalytic domain in complex with IRS1 (625-639) phosphopeptide (pTyr-632, pSer-636)
9EIC 1.58 Å, Crystal structure of unbound N-SH2 domain of SHP2 with T42A mutation
9EHD 1.59 Å, Crystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine phosphorylated peptide…
3B7O 1.6 Å, Crystal structure of the human tyrosine phosphatase SHP2 (PTPN11) with an accessible…
4RDD 1.6 Å, Co-crystal structure of SHP2 in complex with a Cefsulodin derivative

Browse structure collections

About this viewer

MolViewer shows 5X94 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.