8G69: Wildtype PTP1b

Wildtype PTP1b in complex with DES5743. Determined by X-ray diffraction at 1.53 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 1.53 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,278
Mol. weight: 69.99 kDa
Ligands: YXN, MG
Released: 26 Apr 2023

Explore 8G69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G69 contains 25 α-helices and 26 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: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	16-26	11
α-helix	38-43	6
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	189-200	12
β-strand	209	1	2
α-helix	210	1
β-strand	211-214	4	1
α-helix	221-237	17
α-helix	241-243	3
α-helix	246-254	9
α-helix	264-281	18
α-helix	285-288	4

Chain B: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
α-helix	16-26	11
α-helix	38-43	6
β-strand	56-58	3	4
α-helix	59	1
β-strand	66-74	9	4
β-strand	79-84	6	4
α-helix	85-88	4
α-helix	92-102	11
β-strand	104	1	5
β-strand	106-109	4	4
β-strand	114-115	2	6
β-strand	118-119	2	6
β-strand	133-135	3	4
β-strand	140-149	10	4
β-strand	153-162	10	4
β-strand	168-176	9	4
α-helix	189-200	12
β-strand	209	1	5
α-helix	210	1
β-strand	211-214	4	4
α-helix	221-237	17
α-helix	241-243	3
α-helix	246-253	8
α-helix	264-281	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein phosphatase non-receptor type 1	A, B	protein	298	Homo sapiens	P18031 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8G69_1 Tyrosine-protein phosphatase non-receptor type 1 (chains A, B)
MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH
QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLK
CAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWP
DFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKD
PSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED

Ligands and cofactors

ID	Name	Formula	Copies
YXN	4-(5-ethyl-3-methyl-1H-pyrazol-1-yl)aniline	C12 H15 N3	2
MG	Magnesium ion	Mg	1

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

Primary citation

Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. Greisman, J.B., Willmore, L., Yeh, C.Y. et al. J Chem Inf Model (2023) 63:2644-2650. DOI 10.1021/acs.jcim.3c00236 · 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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