5QDK: Tyrosine-protein phosphatase non-receptor type 1

PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000069a. Determined by X-ray diffraction at 1.55 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 1
Atoms: 7,703
Mol. weight: 37.69 kDa
Ligands: JFS
Released: 10 Oct 2018

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

Secondary structure: helices and β-sheets

5QDK contains 13 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: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	16-26	11
α-helix	33-36	4
α-helix	38-43	6
β-strand	56	1	1
α-helix	57-59	3
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	85-88	4
α-helix	92-101	10
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	246-253	8
α-helix	264-280	17

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

>5QDK_1 Tyrosine-protein phosphatase non-receptor type 1 (chains A)
MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLH
QEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLK
CAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWP
DFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKD
PSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLE
PPPEHIPPPPRPPKRILEPHN

Ligands and cofactors

ID	Name	Formula	Copies
JFS	[4-(1H-benzimidazol-1-yl)phenyl]methanol	C14 H12 N2 O	1

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

Primary citation

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. Keedy, D.A., Hill, Z.B., Biel, J.T. et al. Elife (2018) 7. DOI 10.7554/eLife.36307 · 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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