6XEA: PTP1B YopH WPD loop Chimera 3

Crystal Structure of the PTP1B YopH WPD loop Chimera 3 bound to vanadate. Determined by X-ray diffraction at 1.55 Å resolution. Released 15 Dec 2021.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,676
Mol. weight: 37.71 kDa
Ligands: VO4, BEN, MG
Released: 15 Dec 2021

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

Secondary structure: helices and β-sheets

6XEA contains 14 α-helices and 13 β-strands across 1 chain. 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: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
α-helix	16-26	11
α-helix	38-43	6
α-helix	53-55	3
β-strand	56-58	3	1
α-helix	59	1
β-strand	66-74	9	1
β-strand	79-84	6	1
α-helix	85-88	4
α-helix	92-102	11
β-strand	104	1	2
β-strand	106-109	4	1
β-strand	114-115	2	3
β-strand	118-119	2	3
β-strand	133-135	3	1
β-strand	140-149	10	1
β-strand	153-162	10	1
β-strand	168-176	9	1
α-helix	188-200	13
β-strand	209	1	2
α-helix	210	1
β-strand	211-214	4	1
α-helix	221-238	18
α-helix	241-243	3
α-helix	246-253	8
α-helix	264-281	18
α-helix	287-295	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein phosphatase non-receptor type 1	A	protein	321	Homo sapiens	P18031 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XEA_1 Tyrosine-protein phosphatase non-receptor type 1 (chains A)
MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH
QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLK
CAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYGNWP
DQTAPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKD
PSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLE
PPPEHIPPPPRPPKRILEPHN

Ligands and cofactors

ID	Name	Formula	Copies
VO4	Vanadate ion	O4 V	1
BEN	Benzamidine	C7 H8 N2	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (TRS) are not listed.

Primary citation

Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases. Shen, R., Crean, R.M., Olsen, K.J. et al. Chem Sci (2022) 13:13524-13540. DOI 10.1039/d2sc04135a · PubMed

Other PDB entries of the same protein (UniProt P18031 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MN9 1.24 Å, PTP1B 1-284 F225Y-R199N
7MKZ 1.4 Å, PTP1B F225Y mutant, open state
9C66 1.4 Å, Structure of the Mena EVH1 domain bound to the polyproline segment of PTP1B
8U1E 1.43 Å, Apo protein tyrosine phosphatase 1B (PTP1B) at high resolution (1.43 A) in space group…
8G65 1.45 Å, Wildtype PTP1b in complex with DES4799
7MNA 1.47 Å, PTP1B 1-284 F225Y-R199N in complex with TCS401
7MOU 1.48 Å, PTP1B F225Y-R199N-L195R
2CM2 1.5 Å, Structure of Protein Tyrosine Phosphatase 1B (P212121)
7GTW 1.51 Å, PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering,…
7GTX 1.51 Å, PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering,…
5QGF 1.51 Å, PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with…
7GU5 1.52 Å, PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering,…

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