6CMP: Closed structure of inactive SHP2 mutant C459E

Closed structure of inactive SHP2 mutant C459E. Determined by X-ray diffraction at 1.8 Å resolution. Released 14 Nov 2018.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,652
Mol. weight: 122.06 kDa
Released: 14 Nov 2018

Explore 6CMP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CMP contains 40 α-helices and 60 β-strands across 2 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: 20 helices, 32 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	50-58	9	1
β-strand	63-65	3	1
β-strand	70-71	2	1
α-helix	74-83	10
β-strand	89	1	2
β-strand	95	1	2
β-strand	100-101	2	1
β-strand	113-116	4	3
α-helix	119-129	11
β-strand	131	1	4
β-strand	134-139	6	3
β-strand	147-153	7	3
β-strand	157	1	4
β-strand	166-172	7	3
β-strand	173-175	3	5
β-strand	178-180	3	5
β-strand	187	1	5
α-helix	190-199	10
β-strand	202-203	2	6
β-strand	209-210	2	6
β-strand	214-215	2	3
α-helix	216-217	2
β-strand	221-222	2	7
α-helix	223-225	3
α-helix	226-234	9
α-helix	247-255	9
α-helix	258-261	4
α-helix	266-269	4
α-helix	271-274	4
β-strand	289-291	3	8
α-helix	292	1
β-strand	304-310	7	8
β-strand	327-330	4	8
α-helix	331-334	4
α-helix	338-347	10
β-strand	352-355	4	8
α-helix	372-373	2
β-strand	377-380	4	8
β-strand	383-392	10	8
β-strand	396-405	10	8
β-strand	408-420	13	8
α-helix	433-447	15
α-helix	454	1
β-strand	455-458	4	8
α-helix	464-482	19
β-strand	487-488	2	7
α-helix	490-498	9
α-helix	508-526	19

Chain B: 20 helices, 28 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	50-58	9	9
β-strand	63-65	3	9
β-strand	70-71	2	9
α-helix	74-83	10
β-strand	100-101	2	9
β-strand	113-116	4	10
α-helix	119-129	11
β-strand	134-139	6	10
β-strand	147-153	7	10
β-strand	166-172	7	10
β-strand	173-175	3	11
β-strand	178-180	3	11
β-strand	187	1	11
α-helix	190-199	10
β-strand	202-203	2	12
β-strand	209-210	2	12
β-strand	214-215	2	10
α-helix	216-217	2
β-strand	221-222	2	13
α-helix	223-225	3
α-helix	226-234	9
α-helix	247-255	9
α-helix	258-261	4
α-helix	266-269	4
α-helix	271-274	4
β-strand	289-291	3	14
α-helix	292	1
β-strand	304-310	7	14
β-strand	327-330	4	14
α-helix	331-334	4
α-helix	338-347	10
β-strand	352-356	5	14
α-helix	372-373	2
β-strand	377-380	4	14
β-strand	383-392	10	14
β-strand	396-405	10	14
β-strand	408-420	13	14
α-helix	433-447	15
α-helix	454	1
β-strand	455-458	4	14
α-helix	464-482	19
β-strand	487-488	2	13
α-helix	490-498	9
α-helix	508-525	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein phosphatase non-receptor type 11	A, B	protein	532	Homo sapiens	Q06124 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6CMP_1 Tyrosine-protein phosphatase non-receptor type 11 (chains A, B)
GSGMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQ
NTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHL
SGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQEL
KYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLA
ETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDP
NEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTT
KEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQ
YHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHESAGIGRTGTFIVIDILID
IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRI

Primary citation

Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2. Padua, R.A.P., Sun, Y., Marko, I. et al. Nat Commun (2018) 9:4507-4507. DOI 10.1038/s41467-018-06814-w · 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

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